S. pennellii RNAseq simulations

Julin Maloof

July 22, 2016

Introduction

Overall Question

When mapping RNAseq reads from a heterologous species to a reference genome, what is the best way to perform the mapping?

For example:

  • We have a tomato reference genome
  • We want to do RNAseq on a variety of wild relatives of tomato for which we have no genome

Strategy: simulation

  • Use S. pennellii and S. lycopersium. Both are sequenced.
  • Simulate RNASeq reads from S. pennellii and map to S. lycopersicum.
  • Compare actual (simulated) counts to the number of counts that map.
  • And different parameters with those aligners.

Preliminaries

Install Polyester

Use the Polyester package to simulate RNAseq reads. Also see the Polyester paper.

Installation. Only needs to be run once per computer.

source("http://bioconductor.org/biocLite.R")
biocLite("polyester")

Install STAR (only needs to be done once)

brew install rna-star
brew install gcc5 

load libraries and helper scripts

library(polyester)
library(Biostrings)
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
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## Loading required package: stats4
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library(ggplot2)
## Warning: package 'ggplot2' was built under R version 3.2.4
library(Rsamtools)
## Loading required package: GenomeInfoDb
## Loading required package: GenomicRanges
library(rtracklayer)
library(Rsubread)
library(R.utils)
## Loading required package: R.oo
## Loading required package: R.methodsS3
## R.methodsS3 v1.7.0 (2015-02-19) successfully loaded. See ?R.methodsS3 for help.
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library(plyr)
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setwd("~/Documents/Lab Notebook support/2015/rnaseq_simulations")
source("Rnaseq_sim_helper_functions.R")

Simluate reads (simple version)

Load Spen and Slyc transcripts
Spen CDS fasta can be obtained from SGN slyc fasta is also from SGN

pen.transcripts <-  readDNAStringSet("~/Sequences/ref_genomes/S.pen/Spenn-v2-cds-annot.fa")
head(pen.transcripts)
##   A DNAStringSet instance of length 6
##     width seq                                          names               
## [1]   264 ATGCGGGTCTATGAGACTGTA...GGCGAACTGAAAGATCTTAG Sopen00g001010.1 ...
## [2]   294 ATGCCTGTTTTACTAGGCGCG...TTAGCGGGCGACAAGCGTAG Sopen00g001020.1 ...
## [3]   798 ATGATTGAATCTCAGAGGCAT...ATTGGTGGGGAGGTATATGA Sopen00g001030.1 ...
## [4]   693 ATGGAACTTTCTCCCCGAGCT...AAGCGAANGGACGTCGGTAA Sopen00g001040.1 ...
## [5]   951 ATGCCCAATAAAAGTAAAAGA...AGAATAAAGAATTTGAATAG Sopen00g001050.1 ...
## [6]   393 ATGATTTGTTTTATGGACAGT...GTTGCTGCTTCCACAGCTAA Sopen00g001060.1 ...
names(pen.transcripts[1:10])
##  [1] "Sopen00g001010.1 hypothetical protein"                                     
##  [2] "Sopen00g001020.1 hypothetical protein"                                     
##  [3] "Sopen00g001030.1 Cytochrome c oxidase subunit III"                         
##  [4] "Sopen00g001040.1 ATP synthase alpha/beta family, beta-barrel domain"       
##  [5] "Sopen00g001050.1 Mitochondrial ATP synthase B chain precursor (ATP-synt_B)"
##  [6] "Sopen00g001060.1 hypothetical protein"                                     
##  [7] "Sopen00g001070.1 hypothetical protein"                                     
##  [8] "Sopen00g001080.1 hypothetical protein"                                     
##  [9] "Sopen00g001090.1 Reverse transcriptase (RNA-dependent DNA polymerase)"     
## [10] "Sopen00g001100.1 Domain of unknown function (DUF4283)"
lyc.transcripts <- readDNAStringSet("~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.fasta")
head(lyc.transcripts)
##   A DNAStringSet instance of length 6
##     width seq                                          names               
## [1]  1401 ATGTTTGTCCCTTCAATATTT...TTGGCCCTAATATTTGCTAG Solyc00g005000.2....
## [2]   486 ATGTATGTTATATGTAAATGT...CAGTACGTGGATTCAAATAG Solyc00g005020.1....
## [3]   357 ATGGAAGCTGAATACTTCCCT...ATTATCCACTGTTTTTTTAA Solyc00g005040.2....
## [4]   588 ATGGCGGTGAATCCTCAACTA...CATACCAGTCAACCAGCTGA Solyc00g005050.2....
## [5]   273 ATGCTAGTGTGTGTTGGGGTT...TTAAGGCACTACGCCTCTAG Solyc00g005060.1....
## [6]    81 ATGCTTCTAGCTTGGACTGGA...GACTAGCTTCTTATGTTTAG Solyc00g005070.1....
names(lyc.transcripts)[1:10]
##  [1] "Solyc00g005000.2.1 genomic_reference:SL2.50ch00 gene_region:16437-18189 transcript_region:SL2.50ch00:16437..18189+ go_terms:GO:0006508 functional_description:\"Aspartic proteinase nepenthesin I (AHRD V1 **-- A9ZMF9_NEPAL); contains Interpro domain(s)  IPR001461  Peptidase A1 \""
##  [2] "Solyc00g005020.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:68062-68764 transcript_region:SL2.50ch00:68062..68764+ functional_description:\"Unknown Protein (AHRD V1)\""                                                                                     
##  [3] "Solyc00g005040.2.1 genomic_reference:SL2.50ch00 gene_region:550920-551576 transcript_region:SL2.50ch00:550920..551576+ functional_description:\"Potassium channel (AHRD V1 ***- D0EM91_9ROSI); contains Interpro domain(s)  IPR000595  Cyclic nucleotide-binding \""                   
##  [4] "Solyc00g005050.2.1 genomic_reference:SL2.50ch00 gene_region:570544-575454 transcript_region:SL2.50ch00:570544..575454- functional_description:\"Arabinogalactan protein (AHRD V1 ***- B6SST2_MAIZE)\""                                                                                 
##  [5] "Solyc00g005060.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:723746-724018 transcript_region:SL2.50ch00:723746..724018- functional_description:\"Unknown Protein (AHRD V1)\""                                                                                 
##  [6] "Solyc00g005070.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:755300-755543 transcript_region:SL2.50ch00:755300..755543- functional_description:\"Unknown Protein (AHRD V1)\""                                                                                 
##  [7] "Solyc00g005080.1.1 evidence_code:10F0H1E0IEG genomic_reference:SL2.50ch00 gene_region:791493-792010 transcript_region:SL2.50ch00:791493..792010- functional_description:\"Ycf2 (AHRD V1 ***- A6YA23_9MAGN)\""                                                                          
##  [8] "Solyc00g005090.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:1061638-1061922 transcript_region:SL2.50ch00:1061638..1061922- functional_description:\"Unknown Protein (AHRD V1)\""                                                                             
##  [9] "Solyc00g005100.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:1115784-1117712 transcript_region:SL2.50ch00:1115784..1117712+ functional_description:\"Unknown Protein (AHRD V1)\""                                                                             
## [10] "Solyc00g005110.1.1 evidence_code:10F0H0E0IEG genomic_reference:SL2.50ch00 gene_region:1124582-1125325 transcript_region:SL2.50ch00:1124582..1125325- functional_description:\"Unknown Protein (AHRD V1)\""

Reformat names to get rid of description and add Slyc reference

orthologs <- read.delim("Ortho_v2.txt",header=FALSE) #From Tony Bolger
head(orthologs)
##                  V1                 V2
## 1 Sopen03g006680.t1 Solyc04g024690.1.1
## 2 Sopen08g027370.t1 Solyc08g078910.1.1
## 3 Sopen05g001030.t1 Solyc05g005020.2.1
## 4 Sopen03g037380.t1 Solyc03g118500.2.1
## 5 Sopen06g031780.t1 Solyc06g075360.2.1
## 6 Sopen04g003290.t1 Solyc04g008120.1.1
names(orthologs) <- c("PEN","LYC")
orthologs$PEN <- sub("t","",orthologs$PEN)
orthologs$PEN.LYC <- paste(orthologs$PEN,orthologs$LYC,sep="_")
names(pen.transcripts) <- substr(names(pen.transcripts),1,16)
names(pen.transcripts) <- ifelse(!is.na(match(names(pen.transcripts),orthologs$PEN)),
                                 orthologs$PEN.LYC[match(names(pen.transcripts),orthologs$PEN)],
                                 names(pen.transcripts))
pen.transcripts
##   A DNAStringSet instance of length 48923
##         width seq                                      names               
##     [1]   264 ATGCGGGTCTATGAGACTG...CGAACTGAAAGATCTTAG Sopen00g001010.1_...
##     [2]   294 ATGCCTGTTTTACTAGGCG...AGCGGGCGACAAGCGTAG Sopen00g001020.1
##     [3]   798 ATGATTGAATCTCAGAGGC...TGGTGGGGAGGTATATGA Sopen00g001030.1_...
##     [4]   693 ATGGAACTTTCTCCCCGAG...GCGAANGGACGTCGGTAA Sopen00g001040.1_...
##     [5]   951 ATGCCCAATAAAAGTAAAA...AATAAAGAATTTGAATAG Sopen00g001050.1_...
##     ...   ... ...
## [48919]  3924 ATGTCTGCTTTGAACGTGA...AACATCAGAAGCTGTTAA Sopen12g034990.1
## [48920]  3810 ATGGATAGTTCGAAGCTTG...CATCGTGATGAAGGCTGA Sopen12g035000.1
## [48921]   345 ATGAATCTTGGAGGCATAA...ATACAGAGTAAACTTTAG Sopen12g035010.1_...
## [48922]   447 ATGTCGTTAACATATTTTC...GGTCATACTCACACATAA Sopen12g035020.1
## [48923]  6429 ATGGAAGGAAATGAGCATG...AGTCTTGAAACTTTATAA Sopen12g035030.1_...
names(lyc.transcripts) <- substr(names(lyc.transcripts),1,18)
names(lyc.transcripts) <- ifelse(!is.na(match(names(lyc.transcripts),orthologs$LYC)),
                                 orthologs$PEN.LYC[match(names(lyc.transcripts),orthologs$LYC)],
                                 names(lyc.transcripts))
pen.gene.length <- as.integer(nchar(pen.transcripts))
names(pen.gene.length) <- names(pen.transcripts)
lyc.gene.length <- as.integer(nchar(lyc.transcripts))
names(lyc.gene.length) <- names(lyc.transcripts)

Limit ourselves to genes where orthology is clear:

pen.transcripts.small <- pen.transcripts[nchar(names(pen.transcripts))>16]
lyc.transcripts.small <- lyc.transcripts[nchar(names(lyc.transcripts)) > 18]

if(! file.exists("~/Sequences/ref_genomes/S.pen/Spenn-v2-cds-annot_orthlogs_only.fa")) writeXStringSet(pen.transcripts.small,file="~/Sequences/ref_genomes/S.pen/Spenn-v2-cds-annot_orthlogs_only.fa")

if(! file.exists("~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta")) writeXStringSet(lyc.transcripts.small,file="~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta")

Simulate PEN RNAseq reads

#3 minutes for 1M reads
#15 minutes for 5M reads
system.time(
  simulate_experiment(fasta="~/Sequences/ref_genomes/S.pen/Spenn-v2-cds-annot_orthlogs_only.fa",
                      outdir="spen_sim_2",
                      num_reps=1,
                      readlen=45,
                      #line below gives ~ 10M reads, scaled by transcript length and following a rexp distribution
                      reads_per_transcript = round(rexp(n=length(pen.transcripts.small)) * width(pen.transcripts.small) * 
                                                     1e7/ sum(width(pen.transcripts.small) ))+1,
                      paired=FALSE,
                      error_model="illumina5",
                      bias="rnaf"
  )
)
system("sed 's!/!;!' spen_sim_2/sample_01.fasta > spen_sim_2/sample_01_renamed.fasta") #this allows original gene_names to be kept
system("rm spen_sim_2/sample_01.fasta")
system("gzip spen_sim_2/sample_01_renamed.fasta")

Simulate LYC RNAseq reads

system.time(
  simulate_experiment(fasta="~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta",
                      outdir="slyc_sim_2",
                      num_reps=1,
                      readlen=45,
                      #line below gives ~ 10M reads, scaled by transcript length and following a rexp distribution
                      reads_per_transcript = round(rexp(n=length(lyc.transcripts.small)) * width(lyc.transcripts.small) * 
                                                     1e7/ sum(width(lyc.transcripts.small) ))+1,
                      paired=FALSE,
                      error_model="illumina5",
                      bias="rnaf"
  )
)
system("sed 's!/!;!' slyc_sim_2/sample_01.fasta > slyc_sim_2/sample_01_renamed.fasta") #this allows original gene_names to be kept
system("rm slyc_sim_2/sample_01.fasta")
system("gzip slyc_sim_2/sample_01_renamed.fasta")

calculate known counts

Use external python script

pen.known.counts <- read.table(pipe("./CountGene.py spen_sim_2/sample_01_renamed.fasta.gz"),col.names=c("id","count"),stringsAsFactors = FALSE)
pen.known.counts$lyc.id <- substr(pen.known.counts$id,18,33)
head(pen.known.counts)
##                                    id count           lyc.id
## 1 Sopen07g034180.1_Solyc07g065980.2.1  2771 Solyc07g065980.2
## 2 Sopen11g004230.1_Solyc11g008440.1.1   120 Solyc11g008440.1
## 3 Sopen02g006420.1_Solyc02g022830.2.1   746 Solyc02g022830.2
## 4 Sopen08g029390.1_Solyc08g081070.2.1   673 Solyc08g081070.2
## 5 Sopen12g002150.1_Solyc12g006190.1.1   219 Solyc12g006190.1
## 6 Sopen08g024690.1_Solyc08g076040.1.1   279 Solyc08g076040.1
lyc.known.counts <- read.table(pipe("./CountGene.py slyc_sim_2/sample_01_renamed.fasta.gz"),col.names=c("id","count"),stringsAsFactors = FALSE)
lyc.known.counts$lyc.id <- substr(lyc.known.counts$id,18,33)
head(lyc.known.counts)
##                                    id count           lyc.id
## 1 Sopen10g026850.1_Solyc10g062180.1.1   553 Solyc10g062180.1
## 2 Sopen01g052320.1_Solyc01g110160.2.1   233 Solyc01g110160.2
## 3 Sopen03g002160.1_Solyc03g006150.2.1   378 Solyc03g006150.2
## 4 Sopen08g002520.1_Solyc08g006560.2.1  1067 Solyc08g006560.2
## 5 Sopen03g032230.1_Solyc03g113170.1.1   114 Solyc03g113170.1
## 6 Sopen07g030860.1_Solyc07g062630.1.1   697 Solyc07g062630.1

Map with star

Create genome file

Only needs to be done once
This is a shell command
Takes about 25 minutes

gffread -T ITAG2.4_gene_models.gff3 -o ITAG2.4_gene_models.gtf
STAR --runThreadN 6 --runMode genomeGenerate --genomeDir ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/STAR_genome --genomeFastaFiles ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/S_lycopersicum_chromosomes.2.50.fa --sjdbGTFfile ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_gene_models.gtf

Create parameters files

cat > STAR.params.whitney.1
genomeDir /Network/Servers/avalanche.plb.ucdavis.edu/Volumes/Mammoth/Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/STAR_genome
outSAMtype BAM SortedByCoordinate
outSAMunmapped Within
quantMode GeneCounts

Run it!

RunStar(fasta="sample_01_renamed.fasta.gz",prefix = "STAR_1", param.file = "../STAR.params.whitney.1", dir="spen_sim_2",n=12)
RunStar(fasta="sample_01_renamed.fasta.gz",prefix = "STAR_1", param.file = "../STAR.params.whitney.1", dir="slyc_sim_2",n=12)

Evaluate results from STAR

We want to do:

  • correlation between known counts and found counts
  • how many reads map to the wrong gene?
  • how many reads do not map?
  • are the splice junctions correct?

Load in mapped counts

#using the STAR built-in counter
#pen.mapped.counts.STAR <- GetMappedCounts(prefix = "STAR_1", dir = "spen_sim_2")
#lyc.mapped.counts.STAR <- GetMappedCounts(prefix = "STAR_1", dir = "slyc_sim_2")
#using featureCounts from Rsubread
pen.mapped.counts <- GetMappedCounts(prefix = "STAR_1", dir = "spen_sim_2", type="STAR-featureCounts")
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.20.2
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           S spen_sim_2/STAR_1Aligned.sortedByCoord.out ... ||
## ||                                                                            ||
## ||             Output file : ./.Rsubread_featureCounts_pid31851               ||
## ||             Annotations : /Users/jmaloof/Sequences/ref_genomes/tomato/ ... ||
## ||                                                                            ||
## ||                 Threads : 2                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : counted                                          ||
## ||       Read orientations : fr                                               ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2 ... ||
## ||    Features : 160001                                                       ||
## ||    Meta-features : 34725                                                   ||
## ||    Chromosomes/contigs : 13                                                ||
## ||                                                                            ||
## || Process BAM file spen_sim_2/STAR_1Aligned.sortedByCoord.out.bam...         ||
## ||    Single-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 10519873                                                  ||
## ||    Successfully assigned reads : 9117312 (86.7%)                           ||
## ||    Running time : 0.25 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
lyc.mapped.counts <- GetMappedCounts(prefix = "STAR_1", dir = "slyc_sim_2", type="STAR-featureCounts")
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.20.2
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           S slyc_sim_2/STAR_1Aligned.sortedByCoord.out ... ||
## ||                                                                            ||
## ||             Output file : ./.Rsubread_featureCounts_pid31851               ||
## ||             Annotations : /Users/jmaloof/Sequences/ref_genomes/tomato/ ... ||
## ||                                                                            ||
## ||                 Threads : 2                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : counted                                          ||
## ||       Read orientations : fr                                               ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2 ... ||
## ||    Features : 160001                                                       ||
## ||    Meta-features : 34725                                                   ||
## ||    Chromosomes/contigs : 13                                                ||
## ||                                                                            ||
## || Process BAM file slyc_sim_2/STAR_1Aligned.sortedByCoord.out.bam...         ||
## ||    Single-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 10360234                                                  ||
## ||    Successfully assigned reads : 9840016 (95.0%)                           ||
## ||    Running time : 0.28 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//

S. pennellii

Compare known to mapped counts

For many genes this is pretty good, but for some it is pretty poor. Is this due to S. pen?

S. lycopersicum

Compare known to mapped counts

S. lyc maps much better. What is messing up the S. pen mapping?

Investigate…

Lets take a look at the bam file and extract reads from a few genes with 0 mapped reads.

Reads plotted by genes hit and mismatches

Gene length effects

## Warning in self$trans$transform(x): NaNs produced
## Warning: Removed 5271 rows containing missing values (geom_point).

Gene length effects 2

Remove genes

Remove genes with gene length ratio > 1.3 or gene length difference > 300bp

how many reads map to the wrong gene?

mismapping

Total mismapping

with(reads.df.map.single.overlap,sum(mismap) / length(mismap))
## [1] 0.03214682

Of mismaps, what proportion map near to the correct gene:

with(reads.df.map.single.overlap,sum(mapnear & mismap) / sum(mismap))
## [1] 0.696074

Proportion reads mapped to wrong gene (distant):

sum(reads.df.map.single.overlap$mismap[!reads.df.map.single.overlap$mapnear]) / nrow(reads.df.map.single.overlap)
## [1] 0.009770255

why mismapping?

Investigate by looking at where S.pen genes map on S.lyc chromosomes.

Are the S. pen “Orthlogs” really mapping to their cognate S.lyc gene?

Use BLAT to map S. pen predicted cDNAs to S. lyc genome.

Map real reads as comparision

Now look in IGV (Note: Need to use IGVtools to sort and index the .psl file)

head(reads.df.map.single.overlap[reads.df.map.single.overlap$mismap,c("qname","gene.lyc","gene.mapped.to","mapnear")],100)
##                                                                                qname
## 104688   read3816600;Sopen04g012680.1_Solyc04g025530.2.1;mate1:518-562;mate2:723-766
## 104689   read3816832;Sopen04g012680.1_Solyc04g025530.2.1;mate1:723-767;mate2:936-979
## 105406     read69730;Sopen01g001170.1_Solyc01g005140.2.1;mate1:198-242;mate2:381-424
## 107225 read3611020;Sopen04g003410.1_Solyc04g008290.2.1;mate1:840-884;mate2:1073-1116
## 108529   read3609833;Sopen04g003330.1_Solyc04g008210.1.1;mate1:568-612;mate2:809-852
## 116584     read76333;Sopen01g001290.1_Solyc01g005260.2.1;mate1:137-181;mate2:359-402
## 116594     read76843;Sopen01g001290.1_Solyc01g005260.2.1;mate1:128-172;mate2:350-393
## 116595     read76556;Sopen01g001290.1_Solyc01g005260.2.1;mate1:127-171;mate2:369-412
## 116596     read76729;Sopen01g001290.1_Solyc01g005260.2.1;mate1:126-170;mate2:321-364
## 116597     read76737;Sopen01g001290.1_Solyc01g005260.2.1;mate1:125-169;mate2:323-366
## 116598     read76609;Sopen01g001290.1_Solyc01g005260.2.1;mate1:124-168;mate2:359-402
## 116599     read76220;Sopen01g001290.1_Solyc01g005260.2.1;mate1:122-166;mate2:331-374
## 116600     read76235;Sopen01g001290.1_Solyc01g005260.2.1;mate1:122-166;mate2:382-425
## 116653      read76164;Sopen01g001290.1_Solyc01g005260.2.1;mate1:76-120;mate2:276-319
## 116656      read76276;Sopen01g001290.1_Solyc01g005260.2.1;mate1:75-119;mate2:252-295
## 116657      read76944;Sopen01g001290.1_Solyc01g005260.2.1;mate1:75-119;mate2:312-355
## 116658      read76787;Sopen01g001290.1_Solyc01g005260.2.1;mate1:74-118;mate2:290-333
## 116660      read76550;Sopen01g001290.1_Solyc01g005260.2.1;mate1:73-117;mate2:295-338
## 116661      read76804;Sopen01g001290.1_Solyc01g005260.2.1;mate1:73-117;mate2:344-387
## 116662      read76912;Sopen01g001290.1_Solyc01g005260.2.1;mate1:72-116;mate2:234-277
## 116663      read76980;Sopen01g001290.1_Solyc01g005260.2.1;mate1:70-114;mate2:280-323
## 116665      read76533;Sopen01g001290.1_Solyc01g005260.2.1;mate1:68-112;mate2:261-304
## 116666      read76581;Sopen01g001290.1_Solyc01g005260.2.1;mate1:67-111;mate2:267-310
## 116667      read77093;Sopen01g001290.1_Solyc01g005260.2.1;mate1:67-111;mate2:230-273
## 116669      read76548;Sopen01g001290.1_Solyc01g005260.2.1;mate1:66-110;mate2:274-317
## 116670      read77063;Sopen01g001290.1_Solyc01g005260.2.1;mate1:65-109;mate2:280-323
## 116671      read76595;Sopen01g001290.1_Solyc01g005260.2.1;mate1:62-106;mate2:297-340
## 116672      read76219;Sopen01g001290.1_Solyc01g005260.2.1;mate1:61-105;mate2:272-315
## 116700     read77226;Sopen01g001300.1_Solyc01g005270.2.1;mate1:310-354;mate2:455-498
## 116704     read77233;Sopen01g001300.1_Solyc01g005270.2.1;mate1:445-489;mate2:671-714
## 116833     read77216;Sopen01g001300.1_Solyc01g005270.2.1;mate1:402-446;mate2:573-616
## 116834     read77214;Sopen01g001300.1_Solyc01g005270.2.1;mate1:400-444;mate2:567-610
## 116839     read77346;Sopen01g001310.1_Solyc01g005280.2.1;mate1:393-437;mate2:627-670
## 117063 read77828;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1595-1639;mate2:1768-1811
## 117064 read77579;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1469-1513;mate2:1692-1735
## 117065 read77649;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1488-1532;mate2:1691-1734
## 117066 read77915;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1495-1539;mate2:1691-1734
## 117067 read77718;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1462-1506;mate2:1676-1719
## 117068 read77902;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1488-1532;mate2:1674-1717
## 117069 read77961;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1430-1474;mate2:1645-1688
## 117070 read77818;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1430-1474;mate2:1628-1671
## 117071 read77980;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1413-1457;mate2:1612-1655
## 117072 read77628;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1403-1447;mate2:1596-1639
## 117073 read77731;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1421-1465;mate2:1594-1637
## 117074 read77722;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1364-1408;mate2:1583-1626
## 117075 read77963;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1373-1417;mate2:1582-1625
## 117076 read77695;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1558-1602;mate2:1738-1781
## 117077 read77534;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1313-1357;mate2:1556-1599
## 117078 read77884;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1555-1599;mate2:1754-1797
## 117079 read77749;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1331-1375;mate2:1553-1596
## 117080 read77981;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1292-1336;mate2:1541-1584
## 117081 read77560;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1321-1365;mate2:1536-1579
## 117082 read77790;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1338-1382;mate2:1533-1576
## 117083 read77812;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1352-1396;mate2:1531-1574
## 117084 read77771;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1287-1331;mate2:1524-1567
## 117085 read77667;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1303-1347;mate2:1521-1564
## 117086 read77536;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1510-1554;mate2:1739-1782
## 117087 read77894;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1295-1339;mate2:1504-1547
## 117088 read77720;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1302-1346;mate2:1503-1546
## 117089 read77889;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1300-1344;mate2:1503-1546
## 117090 read77760;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1309-1353;mate2:1501-1544
## 117091 read77608;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1491-1535;mate2:1691-1734
## 117092 read77670;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1271-1315;mate2:1490-1533
## 117093 read77832;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1284-1328;mate2:1488-1531
## 117094 read77675;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1312-1356;mate2:1481-1524
## 117095 read77942;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1264-1308;mate2:1473-1516
## 117096 read77687;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1267-1311;mate2:1472-1515
## 117097 read77615;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1218-1262;mate2:1465-1508
## 117098 read77883;Sopen01g001330.1_Solyc01g005310.2.1;mate1:1240-1284;mate2:1459-1502
## 123847     read85096;Sopen01g001610.1_Solyc01g005580.2.1;mate1:279-323;mate2:491-534
## 123848     read85123;Sopen01g001610.1_Solyc01g005580.2.1;mate1:306-350;mate2:489-532
## 123849     read85090;Sopen01g001610.1_Solyc01g005580.2.1;mate1:258-302;mate2:488-531
## 123859     read85125;Sopen01g001610.1_Solyc01g005580.2.1;mate1:167-211;mate2:406-449
## 123860     read85158;Sopen01g001610.1_Solyc01g005580.2.1;mate1:161-205;mate2:393-436
## 124280       read86088;Sopen01g001630.1_Solyc01g005610.2.1;mate1:19-63;mate2:224-267
## 124281       read86983;Sopen01g001630.1_Solyc01g005610.2.1;mate1:18-62;mate2:250-293
## 124282       read87453;Sopen01g001630.1_Solyc01g005610.2.1;mate1:20-64;mate2:201-244
## 124283       read86548;Sopen01g001630.1_Solyc01g005610.2.1;mate1:22-66;mate2:137-180
## 124284       read85545;Sopen01g001630.1_Solyc01g005610.2.1;mate1:26-70;mate2:216-259
## 124285       read86052;Sopen01g001630.1_Solyc01g005610.2.1;mate1:30-74;mate2:268-311
## 124286       read86324;Sopen01g001630.1_Solyc01g005610.2.1;mate1:32-76;mate2:244-287
## 124287       read86779;Sopen01g001630.1_Solyc01g005610.2.1;mate1:32-76;mate2:240-283
## 124288       read87286;Sopen01g001630.1_Solyc01g005610.2.1;mate1:34-78;mate2:191-234
## 124289       read85914;Sopen01g001630.1_Solyc01g005610.2.1;mate1:38-82;mate2:249-292
## 124290       read86006;Sopen01g001630.1_Solyc01g005610.2.1;mate1:38-82;mate2:255-298
## 128661     read93641;Sopen01g001870.1_Solyc01g005760.2.1;mate1:348-392;mate2:552-595
## 128662     read92467;Sopen01g001870.1_Solyc01g005760.2.1;mate1:349-393;mate2:547-590
## 128663     read94196;Sopen01g001870.1_Solyc01g005760.2.1;mate1:351-395;mate2:540-583
## 128677     read89946;Sopen01g001730.1_Solyc01g009690.1.1;mate1:496-540;mate2:668-711
## 128678     read90081;Sopen01g001730.1_Solyc01g009690.1.1;mate1:437-481;mate2:672-715
## 128679     read92304;Sopen01g001870.1_Solyc01g005760.2.1;mate1:358-402;mate2:644-687
## 128680     read92361;Sopen01g001870.1_Solyc01g005760.2.1;mate1:648-692;mate2:860-903
## 128681     read92867;Sopen01g001870.1_Solyc01g005760.2.1;mate1:649-693;mate2:859-902
## 128682     read94365;Sopen01g001870.1_Solyc01g005760.2.1;mate1:648-692;mate2:860-903
## 128685     read89849;Sopen01g001730.1_Solyc01g009690.1.1;mate1:672-716;mate2:888-931
## 128686     read93073;Sopen01g001870.1_Solyc01g005760.2.1;mate1:411-455;mate2:652-695
## 128687     read93527;Sopen01g001870.1_Solyc01g005760.2.1;mate1:651-695;mate2:852-895
## 128688     read92561;Sopen01g001870.1_Solyc01g005760.2.1;mate1:652-696;mate2:851-894
## 128689     read93080;Sopen01g001870.1_Solyc01g005760.2.1;mate1:439-483;mate2:655-698
## 128690     read93299;Sopen01g001870.1_Solyc01g005760.2.1;mate1:439-483;mate2:653-696
##                  gene.lyc     gene.mapped.to mapnear
## 104688 Solyc04g025530.2.1 Solyc01g005000.2.1   FALSE
## 104689 Solyc04g025530.2.1 Solyc01g005000.2.1   FALSE
## 105406 Solyc01g005140.2.1 Solyc01g005030.2.1   FALSE
## 107225 Solyc04g008290.2.1 Solyc01g005080.2.1   FALSE
## 108529 Solyc04g008210.1.1 Solyc01g005120.2.1   FALSE
## 116584 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116594 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116595 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116596 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116597 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116598 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116599 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116600 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116653 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116656 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116657 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116658 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116660 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116661 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116662 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116663 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116665 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116666 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116667 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116669 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116670 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116671 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116672 Solyc01g005260.2.1 Solyc01g005270.2.1    TRUE
## 116700 Solyc01g005270.2.1 Solyc01g005280.2.1    TRUE
## 116704 Solyc01g005270.2.1 Solyc01g005280.2.1    TRUE
## 116833 Solyc01g005270.2.1 Solyc01g005290.2.1    TRUE
## 116834 Solyc01g005270.2.1 Solyc01g005290.2.1    TRUE
## 116839 Solyc01g005280.2.1 Solyc01g005290.2.1    TRUE
## 117063 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117064 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117065 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117066 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117067 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117068 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117069 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117070 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117071 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117072 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117073 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117074 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117075 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117076 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117077 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117078 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117079 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117080 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117081 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117082 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117083 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117084 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117085 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117086 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117087 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117088 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117089 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117090 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117091 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117092 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117093 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117094 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117095 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117096 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117097 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 117098 Solyc01g005310.2.1 Solyc01g005300.2.1    TRUE
## 123847 Solyc01g005580.2.1 Solyc01g005570.2.1    TRUE
## 123848 Solyc01g005580.2.1 Solyc01g005570.2.1    TRUE
## 123849 Solyc01g005580.2.1 Solyc01g005570.2.1    TRUE
## 123859 Solyc01g005580.2.1 Solyc01g005570.2.1    TRUE
## 123860 Solyc01g005580.2.1 Solyc01g005570.2.1    TRUE
## 124280 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124281 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124282 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124283 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124284 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124285 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124286 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124287 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124288 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124289 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 124290 Solyc01g005610.2.1 Solyc01g005600.2.1    TRUE
## 128661 Solyc01g005760.2.1 Solyc01g005710.2.1   FALSE
## 128662 Solyc01g005760.2.1 Solyc01g005710.2.1   FALSE
## 128663 Solyc01g005760.2.1 Solyc01g005710.2.1   FALSE
## 128677 Solyc01g009690.1.1 Solyc01g005720.2.1   FALSE
## 128678 Solyc01g009690.1.1 Solyc01g005720.2.1   FALSE
## 128679 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128680 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128681 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128682 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128685 Solyc01g009690.1.1 Solyc01g005720.2.1   FALSE
## 128686 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128687 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128688 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128689 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
## 128690 Solyc01g005760.2.1 Solyc01g005720.2.1   FALSE
sort(table(reads.df.map.single.overlap$gene.lyc[reads.df.map.single.overlap$mismap]))
## 
## Solyc01g005060.2.1 Solyc01g005140.2.1 Solyc01g005280.2.1 
##                  1                  1                  1 
## Solyc01g006120.2.1 Solyc01g006440.1.1 Solyc01g006490.2.1 
##                  1                  1                  1 
## Solyc01g006730.2.1 Solyc01g007070.2.1 Solyc01g007330.2.1 
##                  1                  1                  1 
## Solyc01g007340.2.1 Solyc01g008530.2.1 Solyc01g008640.2.1 
##                  1                  1                  1 
## Solyc01g008690.2.1 Solyc01g008840.2.1 Solyc01g009300.2.1 
##                  1                  1                  1 
## Solyc01g009360.1.1 Solyc01g009420.2.1 Solyc01g009530.1.1 
##                  1                  1                  1 
## Solyc01g010480.2.1 Solyc01g028930.2.1 Solyc01g044510.1.1 
##                  1                  1                  1 
## Solyc01g060020.2.1 Solyc01g066250.1.1 Solyc01g066620.2.1 
##                  1                  1                  1 
## Solyc01g067960.1.1 Solyc01g068150.2.1 Solyc01g068550.2.1 
##                  1                  1                  1 
## Solyc01g073750.2.1 Solyc01g073840.1.1 Solyc01g079670.2.1 
##                  1                  1                  1 
## Solyc01g079750.2.1 Solyc01g080910.2.1 Solyc01g081100.1.1 
##                  1                  1                  1 
## Solyc01g086990.2.1 Solyc01g087430.2.1 Solyc01g087680.2.1 
##                  1                  1                  1 
## Solyc01g088560.2.1 Solyc01g090430.2.1 Solyc01g090820.1.1 
##                  1                  1                  1 
## Solyc01g090990.2.1 Solyc01g091690.2.1 Solyc01g094070.2.1 
##                  1                  1                  1 
## Solyc01g094080.2.1 Solyc01g095100.2.1 Solyc01g095490.2.1 
##                  1                  1                  1 
## Solyc01g095830.2.1 Solyc01g095960.2.1 Solyc01g097610.2.1 
##                  1                  1                  1 
## Solyc01g098590.2.1 Solyc01g099200.2.1 Solyc01g099390.2.1 
##                  1                  1                  1 
## Solyc01g100530.2.1 Solyc01g100570.2.1 Solyc01g100800.1.1 
##                  1                  1                  1 
## Solyc01g103140.2.1 Solyc01g104800.2.1 Solyc01g105030.2.1 
##                  1                  1                  1 
## Solyc01g105050.2.1 Solyc01g106480.2.1 Solyc01g106750.1.1 
##                  1                  1                  1 
## Solyc01g107930.2.1 Solyc01g107960.2.1 Solyc01g108010.2.1 
##                  1                  1                  1 
## Solyc01g108940.1.1 Solyc01g109490.2.1 Solyc01g111340.2.1 
##                  1                  1                  1 
## Solyc01g111440.2.1 Solyc01g111640.2.1 Solyc01g111900.2.1 
##                  1                  1                  1 
## Solyc01g111980.2.1 Solyc01g112100.2.1 Solyc02g021680.2.1 
##                  1                  1                  1 
## Solyc02g031790.1.1 Solyc02g032330.2.1 Solyc02g032730.1.1 
##                  1                  1                  1 
## Solyc02g036230.1.1 Solyc02g036450.2.1 Solyc02g061960.2.1 
##                  1                  1                  1 
## Solyc02g062670.2.1 Solyc02g062740.2.1 Solyc02g063170.2.1 
##                  1                  1                  1 
## Solyc02g063220.2.1 Solyc02g065230.2.1 Solyc02g065740.2.1 
##                  1                  1                  1 
## Solyc02g066980.1.1 Solyc02g067040.2.1 Solyc02g067570.2.1 
##                  1                  1                  1 
## Solyc02g068430.2.1 Solyc02g068590.2.1 Solyc02g069650.1.1 
##                  1                  1                  1 
## Solyc02g070200.1.1 Solyc02g071350.2.1 Solyc02g071540.1.1 
##                  1                  1                  1 
## Solyc02g072050.1.1 Solyc02g072190.2.1 Solyc02g077030.2.1 
##                  1                  1                  1 
## Solyc02g077390.1.1 Solyc02g078840.2.1 Solyc02g079040.2.1 
##                  1                  1                  1 
## Solyc02g079540.1.1 Solyc02g080800.2.1 Solyc02g082110.2.1 
##                  1                  1                  1 
## Solyc02g082320.1.1 Solyc02g082720.2.1 Solyc02g083700.2.1 
##                  1                  1                  1 
## Solyc02g084110.1.1 Solyc02g084960.1.1 Solyc02g085500.2.1 
##                  1                  1                  1 
## Solyc02g086180.2.1 Solyc02g087030.1.1 Solyc02g087790.1.1 
##                  1                  1                  1 
## Solyc02g087950.2.1 Solyc02g088320.2.1 Solyc02g088670.1.1 
##                  1                  1                  1 
## Solyc02g089620.2.1 Solyc02g090510.2.1 Solyc02g090730.2.1 
##                  1                  1                  1 
## Solyc02g091470.2.1 Solyc02g091580.2.1 Solyc02g093320.2.1 
##                  1                  1                  1 
## Solyc02g093330.2.1 Solyc02g093500.2.1 Solyc03g005080.2.1 
##                  1                  1                  1 
## Solyc03g005560.1.1 Solyc03g005920.2.1 Solyc03g006530.2.1 
##                  1                  1                  1 
## Solyc03g006840.2.1 Solyc03g019660.2.1 Solyc03g025670.2.1 
##                  1                  1                  1 
## Solyc03g026020.2.1 Solyc03g031490.2.1 Solyc03g032020.2.1 
##                  1                  1                  1 
## Solyc03g033690.1.1 Solyc03g033790.2.1 Solyc03g033820.1.1 
##                  1                  1                  1 
## Solyc03g034270.2.1 Solyc03g043580.1.1 Solyc03g043930.2.1 
##                  1                  1                  1 
## Solyc03g046420.1.1 Solyc03g059420.2.1 Solyc03g063300.1.1 
##                  1                  1                  1 
## Solyc03g071550.1.1 Solyc03g078260.2.1 Solyc03g078520.2.1 
##                  1                  1                  1 
## Solyc03g080070.2.1 Solyc03g082390.2.1 Solyc03g082620.2.1 
##                  1                  1                  1 
## Solyc03g082750.1.1 Solyc03g083270.2.1 Solyc03g083390.2.1 
##                  1                  1                  1 
## Solyc03g083820.1.1 Solyc03g093890.2.1 Solyc03g095500.2.1 
##                  1                  1                  1 
## Solyc03g095980.2.1 Solyc03g096900.2.1 Solyc03g098200.2.1 
##                  1                  1                  1 
## Solyc03g098640.2.1 Solyc03g111860.1.1 Solyc03g112300.2.1 
##                  1                  1                  1 
## Solyc03g113040.2.1 Solyc03g113060.2.1 Solyc03g113410.1.1 
##                  1                  1                  1 
## Solyc03g113580.1.1 Solyc03g113800.2.1 Solyc03g114400.2.1 
##                  1                  1                  1 
## Solyc03g114850.2.1 Solyc03g115120.1.1 Solyc03g115840.2.1 
##                  1                  1                  1 
## Solyc03g116380.2.1 Solyc03g117170.1.1 Solyc03g117820.1.1 
##                  1                  1                  1 
## Solyc03g118090.2.1 Solyc03g119150.2.1 Solyc03g119390.2.1 
##                  1                  1                  1 
## Solyc03g120210.1.1 Solyc03g120470.2.1 Solyc03g120520.1.1 
##                  1                  1                  1 
## Solyc03g120970.2.1 Solyc03g121410.2.1 Solyc03g121570.2.1 
##                  1                  1                  1 
## Solyc03g121590.2.1 Solyc03g121980.2.1 Solyc04g005720.2.1 
##                  1                  1                  1 
## Solyc04g007650.2.1 Solyc04g007680.2.1 Solyc04g007750.2.1 
##                  1                  1                  1 
## Solyc04g008010.2.1 Solyc04g008210.1.1 Solyc04g008290.2.1 
##                  1                  1                  1 
## Solyc04g008560.2.1 Solyc04g009620.2.1 Solyc04g009640.2.1 
##                  1                  1                  1 
## Solyc04g009820.2.1 Solyc04g010260.2.1 Solyc04g011350.2.1 
##                  1                  1                  1 
## Solyc04g011720.2.1 Solyc04g014270.2.1 Solyc04g014470.2.1 
##                  1                  1                  1 
## Solyc04g018210.1.1 Solyc04g025880.2.1 Solyc04g039640.2.1 
##                  1                  1                  1 
## Solyc04g050010.1.1 Solyc04g050730.2.1 Solyc04g050750.1.1 
##                  1                  1                  1 
## Solyc04g056460.1.1 Solyc04g064680.2.1 Solyc04g064860.1.1 
##                  1                  1                  1 
## Solyc04g071080.1.1 Solyc04g071750.2.1 Solyc04g074360.1.1 
##                  1                  1                  1 
## Solyc04g074930.2.1 Solyc04g076220.2.1 Solyc04g076230.2.1 
##                  1                  1                  1 
## Solyc04g076650.1.1 Solyc04g077360.2.1 Solyc04g077890.1.1 
##                  1                  1                  1 
## Solyc04g078130.2.1 Solyc04g078160.2.1 Solyc04g079070.2.1 
##                  1                  1                  1 
## Solyc04g079530.2.1 Solyc04g080300.2.1 Solyc04g081200.2.1 
##                  1                  1                  1 
## Solyc04g082220.1.1 Solyc04g082290.2.1 Solyc04g082630.2.1 
##                  1                  1                  1 
## Solyc04g082980.1.1 Solyc05g005130.1.1 Solyc05g005710.2.1 
##                  1                  1                  1 
## Solyc05g005910.2.1 Solyc05g006130.2.1 Solyc05g006210.2.1 
##                  1                  1                  1 
## Solyc05g007000.2.1 Solyc05g007660.2.1 Solyc05g009230.1.1 
##                  1                  1                  1 
## Solyc05g009400.1.1 Solyc05g010010.1.1 Solyc05g010220.1.1 
##                  1                  1                  1 
## Solyc05g010460.2.1 Solyc05g012050.2.1 Solyc05g013040.2.1 
##                  1                  1                  1 
## Solyc05g013160.2.1 Solyc05g013280.2.1 Solyc05g013340.2.1 
##                  1                  1                  1 
## Solyc05g013770.2.1 Solyc05g014470.2.1 Solyc05g015160.2.1 
##                  1                  1                  1 
## Solyc05g015270.1.1 Solyc05g015550.1.1 Solyc05g017760.2.1 
##                  1                  1                  1 
## Solyc05g017890.2.1 Solyc05g018340.2.1 Solyc05g021100.2.1 
##                  1                  1                  1 
## Solyc05g023850.1.1 Solyc05g050120.2.1 Solyc05g050740.2.1 
##                  1                  1                  1 
## Solyc05g051530.2.1 Solyc05g051900.2.1 Solyc05g052400.2.1 
##                  1                  1                  1 
## Solyc05g053120.1.1 Solyc05g053550.2.1 Solyc05g053740.2.1 
##                  1                  1                  1 
## Solyc05g053940.2.1 Solyc05g054310.2.1 Solyc05g054370.2.1 
##                  1                  1                  1 
## Solyc05g055470.2.1 Solyc05g056430.1.1 Solyc06g007980.2.1 
##                  1                  1                  1 
## Solyc06g008340.2.1 Solyc06g008750.1.1 Solyc06g008960.2.1 
##                  1                  1                  1 
## Solyc06g009270.2.1 Solyc06g009540.1.1 Solyc06g011500.1.1 
##                  1                  1                  1 
## Solyc06g018070.1.1 Solyc06g034200.1.1 Solyc06g035530.2.1 
##                  1                  1                  1 
## Solyc06g036810.1.1 Solyc06g048890.2.1 Solyc06g048910.1.1 
##                  1                  1                  1 
## Solyc06g050160.2.1 Solyc06g051850.1.1 Solyc06g053160.2.1 
##                  1                  1                  1 
## Solyc06g053740.2.1 Solyc06g054480.2.1 Solyc06g060920.2.1 
##                  1                  1                  1 
## Solyc06g061280.2.1 Solyc06g062390.2.1 Solyc06g062830.2.1 
##                  1                  1                  1 
## Solyc06g062860.2.1 Solyc06g062970.1.1 Solyc06g063010.2.1 
##                  1                  1                  1 
## Solyc06g063150.2.1 Solyc06g065910.2.1 Solyc06g066000.1.1 
##                  1                  1                  1 
## Solyc06g066390.1.1 Solyc06g067920.2.1 Solyc06g068080.2.1 
##                  1                  1                  1 
## Solyc06g068830.1.1 Solyc06g068980.2.1 Solyc06g069550.1.1 
##                  1                  1                  1 
## Solyc06g069810.1.1 Solyc06g069870.2.1 Solyc06g071570.2.1 
##                  1                  1                  1 
## Solyc06g071650.1.1 Solyc06g071920.2.1 Solyc06g071990.2.1 
##                  1                  1                  1 
## Solyc06g072810.2.1 Solyc06g072880.1.1 Solyc06g073950.2.1 
##                  1                  1                  1 
## Solyc06g074390.2.1 Solyc06g074670.2.1 Solyc06g074850.2.1 
##                  1                  1                  1 
## Solyc06g074890.1.1 Solyc06g075400.2.1 Solyc06g075480.2.1 
##                  1                  1                  1 
## Solyc06g075570.1.1 Solyc06g075710.1.1 Solyc06g075720.1.1 
##                  1                  1                  1 
## Solyc06g076980.2.1 Solyc06g083140.2.1 Solyc06g083760.2.1 
##                  1                  1                  1 
## Solyc06g083830.2.1 Solyc07g005560.2.1 Solyc07g005730.2.1 
##                  1                  1                  1 
## Solyc07g005780.1.1 Solyc07g007730.2.1 Solyc07g008300.1.1 
##                  1                  1                  1 
## Solyc07g008880.2.1 Solyc07g014660.1.1 Solyc07g016210.1.1 
##                  1                  1                  1 
## Solyc07g025270.1.1 Solyc07g045300.2.1 Solyc07g045430.2.1 
##                  1                  1                  1 
## Solyc07g048070.2.1 Solyc07g049700.1.1 Solyc07g052760.1.1 
##                  1                  1                  1 
## Solyc07g052870.1.1 Solyc07g053570.2.1 Solyc07g053870.2.1 
##                  1                  1                  1 
## Solyc07g054320.2.1 Solyc07g055730.2.1 Solyc07g056100.1.1 
##                  1                  1                  1 
## Solyc07g062010.1.1 Solyc07g062360.1.1 Solyc07g062430.2.1 
##                  1                  1                  1 
## Solyc07g062580.2.1 Solyc07g063580.2.1 Solyc07g063820.2.1 
##                  1                  1                  1 
## Solyc07g063940.1.1 Solyc07g064030.2.1 Solyc07g064340.2.1 
##                  1                  1                  1 
## Solyc07g064400.1.1 Solyc07g064420.2.1 Solyc07g064520.2.1 
##                  1                  1                  1 
## Solyc07g065760.1.1 Solyc07g066500.1.1 Solyc08g005550.2.1 
##                  1                  1                  1 
## Solyc08g006450.1.1 Solyc08g006910.2.1 Solyc08g007270.2.1 
##                  1                  1                  1 
## Solyc08g007530.2.1 Solyc08g007680.1.1 Solyc08g008410.2.1 
##                  1                  1                  1 
## Solyc08g008480.2.1 Solyc08g014150.2.1 Solyc08g014190.2.1 
##                  1                  1                  1 
## Solyc08g014550.2.1 Solyc08g015990.2.1 Solyc08g016470.1.1 
##                  1                  1                  1 
## Solyc08g022130.1.1 Solyc08g048170.1.1 Solyc08g061430.1.1 
##                  1                  1                  1 
## Solyc08g061610.2.1 Solyc08g061650.2.1 Solyc08g061930.2.1 
##                  1                  1                  1 
## Solyc08g065490.2.1 Solyc08g065780.1.1 Solyc08g065890.2.1 
##                  1                  1                  1 
## Solyc08g066580.2.1 Solyc08g066990.2.1 Solyc08g068380.2.1 
##                  1                  1                  1 
## Solyc08g075710.2.1 Solyc08g075830.2.1 Solyc08g076140.2.1 
##                  1                  1                  1 
## Solyc08g076790.2.1 Solyc08g076970.2.1 Solyc08g076990.2.1 
##                  1                  1                  1 
## Solyc08g077690.2.1 Solyc08g077820.2.1 Solyc08g078290.1.1 
##                  1                  1                  1 
## Solyc08g078310.2.1 Solyc08g078590.1.1 Solyc08g080170.2.1 
##                  1                  1                  1 
## Solyc08g080510.2.1 Solyc08g081360.2.1 Solyc08g082900.2.1 
##                  1                  1                  1 
## Solyc08g083040.2.1 Solyc08g083370.2.1 Solyc09g005150.1.1 
##                  1                  1                  1 
## Solyc09g005830.1.1 Solyc09g007590.1.1 Solyc09g007630.2.1 
##                  1                  1                  1 
## Solyc09g008440.1.1 Solyc09g008740.1.1 Solyc09g008770.2.1 
##                  1                  1                  1 
## Solyc09g008960.1.1 Solyc09g009200.1.1 Solyc09g009540.2.1 
##                  1                  1                  1 
## Solyc09g009600.1.1 Solyc09g009690.2.1 Solyc09g010080.2.1 
##                  1                  1                  1 
## Solyc09g010450.1.1 Solyc09g011060.2.1 Solyc09g011580.2.1 
##                  1                  1                  1 
## Solyc09g014590.2.1 Solyc09g015120.2.1 Solyc09g015850.2.1 
##                  1                  1                  1 
## Solyc09g018730.2.1 Solyc09g018960.2.1 Solyc09g020130.2.1 
##                  1                  1                  1 
## Solyc09g025220.1.1 Solyc09g025280.1.1 Solyc09g055600.1.1 
##                  1                  1                  1 
## Solyc09g061430.2.1 Solyc09g064290.1.1 Solyc09g064330.1.1 
##                  1                  1                  1 
## Solyc09g065410.2.1 Solyc09g066090.2.1 Solyc09g072690.1.1 
##                  1                  1                  1 
## Solyc09g072900.2.1 Solyc09g074350.1.1 Solyc09g074670.2.1 
##                  1                  1                  1 
## Solyc09g075770.1.1 Solyc09g075830.2.1 Solyc09g082140.2.1 
##                  1                  1                  1 
## Solyc09g082760.2.1 Solyc09g083000.2.1 Solyc09g089520.2.1 
##                  1                  1                  1 
## Solyc09g089770.2.1 Solyc09g090130.2.1 Solyc09g090500.2.1 
##                  1                  1                  1 
## Solyc09g090580.2.1 Solyc09g091090.1.1 Solyc09g091660.2.1 
##                  1                  1                  1 
## Solyc09g098210.1.1 Solyc10g005400.2.1 Solyc10g005440.1.1 
##                  1                  1                  1 
## Solyc10g005840.2.1 Solyc10g005920.2.1 Solyc10g006100.2.1 
##                  1                  1                  1 
## Solyc10g006110.2.1 Solyc10g006660.2.1 Solyc10g007350.2.1 
##                  1                  1                  1 
## Solyc10g007440.2.1 Solyc10g007630.1.1 Solyc10g008260.1.1 
##                  1                  1                  1 
## Solyc10g008410.1.1 Solyc10g008640.2.1 Solyc10g008910.1.1 
##                  1                  1                  1 
## Solyc10g008980.2.1 Solyc10g011760.2.1 Solyc10g017650.1.1 
##                  1                  1                  1 
## Solyc10g017850.2.1 Solyc10g018790.1.1 Solyc10g038130.1.1 
##                  1                  1                  1 
## Solyc10g045180.1.1 Solyc10g045260.1.1 Solyc10g047110.1.1 
##                  1                  1                  1 
## Solyc10g047820.1.1 Solyc10g050570.1.1 Solyc10g050690.1.1 
##                  1                  1                  1 
## Solyc10g053900.1.1 Solyc10g054010.1.1 Solyc10g054030.1.1 
##                  1                  1                  1 
## Solyc10g055450.1.1 Solyc10g061920.1.1 Solyc10g062180.1.1 
##                  1                  1                  1 
## Solyc10g075040.1.1 Solyc10g076660.1.1 Solyc10g076690.1.1 
##                  1                  1                  1 
## Solyc10g078260.1.1 Solyc10g078390.1.1 Solyc10g078990.1.1 
##                  1                  1                  1 
## Solyc10g079190.1.1 Solyc10g079240.1.1 Solyc10g079370.1.1 
##                  1                  1                  1 
## Solyc10g079680.1.1 Solyc10g080870.2.1 Solyc10g081030.1.1 
##                  1                  1                  1 
## Solyc10g081200.1.1 Solyc10g082020.1.1 Solyc10g083440.1.1 
##                  1                  1                  1 
## Solyc10g084080.1.1 Solyc10g085220.1.1 Solyc10g085410.1.1 
##                  1                  1                  1 
## Solyc10g085710.1.1 Solyc10g085790.1.1 Solyc10g086020.1.1 
##                  1                  1                  1 
## Solyc10g086380.1.1 Solyc10g086640.1.1 Solyc11g005330.1.1 
##                  1                  1                  1 
## Solyc11g006180.1.1 Solyc11g007040.1.1 Solyc11g007370.1.1 
##                  1                  1                  1 
## Solyc11g007480.1.1 Solyc11g007960.1.1 Solyc11g008140.1.1 
##                  1                  1                  1 
## Solyc11g008230.1.1 Solyc11g008520.1.1 Solyc11g010540.1.1 
##                  1                  1                  1 
## Solyc11g011090.1.1 Solyc11g012510.1.1 Solyc11g012540.1.1 
##                  1                  1                  1 
## Solyc11g012690.1.1 Solyc11g013530.1.1 Solyc11g019990.1.1 
##                  1                  1                  1 
## Solyc11g020620.1.1 Solyc11g021020.1.1 Solyc11g021340.1.1 
##                  1                  1                  1 
## Solyc11g027660.1.1 Solyc11g044860.1.1 Solyc11g044880.1.1 
##                  1                  1                  1 
## Solyc11g050840.1.1 Solyc11g056360.1.1 Solyc11g062070.1.1 
##                  1                  1                  1 
## Solyc11g065140.1.1 Solyc11g065910.1.1 Solyc11g066240.1.1 
##                  1                  1                  1 
## Solyc11g066560.1.1 Solyc11g069950.1.1 Solyc11g070120.1.1 
##                  1                  1                  1 
## Solyc11g072650.1.1 Solyc11g072910.1.1 Solyc11g073090.1.1 
##                  1                  1                  1 
## Solyc12g005160.1.1 Solyc12g005170.1.1 Solyc12g005290.1.1 
##                  1                  1                  1 
## Solyc12g005470.1.1 Solyc12g005860.1.1 Solyc12g005870.1.1 
##                  1                  1                  1 
## Solyc12g006060.1.1 Solyc12g006370.1.1 Solyc12g006380.1.1 
##                  1                  1                  1 
## Solyc12g006680.1.1 Solyc12g006950.1.1 Solyc12g008840.1.1 
##                  1                  1                  1 
## Solyc12g008890.1.1 Solyc12g009400.1.1 Solyc12g009610.1.1 
##                  1                  1                  1 
## Solyc12g010520.1.1 Solyc12g011390.1.1 Solyc12g013710.1.1 
##                  1                  1                  1 
## Solyc12g014150.1.1 Solyc12g017900.1.1 Solyc12g019310.1.1 
##                  1                  1                  1 
## Solyc12g038390.1.1 Solyc12g038820.1.1 Solyc12g042070.1.1 
##                  1                  1                  1 
## Solyc12g042750.1.1 Solyc12g042960.1.1 Solyc12g044640.1.1 
##                  1                  1                  1 
## Solyc12g055820.1.1 Solyc12g056380.1.1 Solyc12g056430.1.1 
##                  1                  1                  1 
## Solyc12g077350.1.1 Solyc12g087830.1.1 Solyc12g089210.1.1 
##                  1                  1                  1 
## Solyc12g089250.1.1 Solyc12g094470.1.1 Solyc12g095840.1.1 
##                  1                  1                  1 
## Solyc12g095860.1.1 Solyc12g096140.1.1 Solyc12g096300.1.1 
##                  1                  1                  1 
## Solyc12g096830.1.1 Solyc12g096860.1.1 Solyc12g098210.1.1 
##                  1                  1                  1 
## Solyc12g098580.1.1 Solyc12g098680.1.1 Solyc12g100120.1.1 
##                  1                  1                  1 
## Solyc12g100270.1.1 Solyc01g005850.1.1 Solyc01g006620.2.1 
##                  1                  2                  2 
## Solyc01g007020.2.1 Solyc01g007640.2.1 Solyc01g008060.2.1 
##                  2                  2                  2 
## Solyc01g008710.2.1 Solyc01g009050.2.1 Solyc01g009770.2.1 
##                  2                  2                  2 
## Solyc01g016690.1.1 Solyc01g057890.1.1 Solyc01g057960.1.1 
##                  2                  2                  2 
## Solyc01g059880.2.1 Solyc01g066970.2.1 Solyc01g067100.2.1 
##                  2                  2                  2 
## Solyc01g068430.1.1 Solyc01g079580.2.1 Solyc01g080930.2.1 
##                  2                  2                  2 
## Solyc01g081010.2.1 Solyc01g081180.1.1 Solyc01g087150.2.1 
##                  2                  2                  2 
## Solyc01g090730.2.1 Solyc01g094030.2.1 Solyc01g094370.2.1 
##                  2                  2                  2 
## Solyc01g096940.2.1 Solyc01g098530.2.1 Solyc01g098560.2.1 
##                  2                  2                  2 
## Solyc01g099010.2.1 Solyc01g100610.2.1 Solyc01g103630.2.1 
##                  2                  2                  2 
## Solyc01g103830.1.1 Solyc01g105350.1.1 Solyc01g106250.2.1 
##                  2                  2                  2 
## Solyc01g106790.2.1 Solyc01g107100.2.1 Solyc01g107510.2.1 
##                  2                  2                  2 
## Solyc01g107650.2.1 Solyc01g108110.2.1 Solyc01g108560.2.1 
##                  2                  2                  2 
## Solyc01g109150.2.1 Solyc01g109940.2.1 Solyc01g110200.1.1 
##                  2                  2                  2 
## Solyc01g110750.2.1 Solyc01g111310.2.1 Solyc02g005350.2.1 
##                  2                  2                  2 
## Solyc02g021580.1.1 Solyc02g031950.2.1 Solyc02g032210.1.1 
##                  2                  2                  2 
## Solyc02g062570.2.1 Solyc02g063260.2.1 Solyc02g065150.1.1 
##                  2                  2                  2 
## Solyc02g065300.1.1 Solyc02g071820.2.1 Solyc02g071870.2.1 
##                  2                  2                  2 
## Solyc02g072280.1.1 Solyc02g077270.2.1 Solyc02g080440.2.1 
##                  2                  2                  2 
## Solyc02g083040.1.1 Solyc02g083150.2.1 Solyc02g084240.2.1 
##                  2                  2                  2 
## Solyc02g084390.2.1 Solyc02g085870.2.1 Solyc02g086230.1.1 
##                  2                  2                  2 
## Solyc02g086460.2.1 Solyc02g086940.2.1 Solyc02g087450.2.1 
##                  2                  2                  2 
## Solyc02g088770.2.1 Solyc02g089160.2.1 Solyc02g089670.2.1 
##                  2                  2                  2 
## Solyc02g091240.1.1 Solyc02g093040.2.1 Solyc03g005620.2.1 
##                  2                  2                  2 
## Solyc03g005680.2.1 Solyc03g005720.2.1 Solyc03g005750.2.1 
##                  2                  2                  2 
## Solyc03g006260.2.1 Solyc03g006620.2.1 Solyc03g019900.2.1 
##                  2                  2                  2 
## Solyc03g025140.1.1 Solyc03g025450.2.1 Solyc03g032010.2.1 
##                  2                  2                  2 
## Solyc03g033540.2.1 Solyc03g033950.2.1 Solyc03g063680.1.1 
##                  2                  2                  2 
## Solyc03g071760.1.1 Solyc03g078060.2.1 Solyc03g080000.1.1 
##                  2                  2                  2 
## Solyc03g082760.1.1 Solyc03g093270.2.1 Solyc03g093870.1.1 
##                  2                  2                  2 
## Solyc03g093930.2.1 Solyc03g094040.2.1 Solyc03g095270.1.1 
##                  2                  2                  2 
## Solyc03g095620.2.1 Solyc03g096000.2.1 Solyc03g096530.1.1 
##                  2                  2                  2 
## Solyc03g111350.2.1 Solyc03g111450.1.1 Solyc03g114000.2.1 
##                  2                  2                  2 
## Solyc03g114280.2.1 Solyc03g119420.2.1 Solyc03g121360.1.1 
##                  2                  2                  2 
## Solyc03g122140.2.1 Solyc03g123600.2.1 Solyc04g005560.2.1 
##                  2                  2                  2 
## Solyc04g007360.1.1 Solyc04g008720.2.1 Solyc04g011570.2.1 
##                  2                  2                  2 
## Solyc04g012060.2.1 Solyc04g016160.2.1 Solyc04g016490.2.1 
##                  2                  2                  2 
## Solyc04g025530.2.1 Solyc04g025900.1.1 Solyc04g050770.1.1 
##                  2                  2                  2 
## Solyc04g052980.1.1 Solyc04g072450.2.1 Solyc04g072520.1.1 
##                  2                  2                  2 
## Solyc04g076660.2.1 Solyc04g079180.2.1 Solyc04g079830.2.1 
##                  2                  2                  2 
## Solyc04g080360.2.1 Solyc04g081690.1.1 Solyc04g081910.2.1 
##                  2                  2                  2 
## Solyc04g082040.2.1 Solyc05g005110.1.1 Solyc05g005190.2.1 
##                  2                  2                  2 
## Solyc05g005340.2.1 Solyc05g005390.1.1 Solyc05g006590.2.1 
##                  2                  2                  2 
## Solyc05g007050.2.1 Solyc05g007640.2.1 Solyc05g009660.2.1 
##                  2                  2                  2 
## Solyc05g014120.1.1 Solyc05g014150.2.1 Solyc05g014160.2.1 
##                  2                  2                  2 
## Solyc05g025510.2.1 Solyc05g041200.2.1 Solyc05g043360.1.1 
##                  2                  2                  2 
## Solyc05g050230.2.1 Solyc05g050350.1.1 Solyc05g050670.1.1 
##                  2                  2                  2 
## Solyc05g051660.1.1 Solyc05g052340.2.1 Solyc05g052740.1.1 
##                  2                  2                  2 
## Solyc05g052830.2.1 Solyc05g053830.2.1 Solyc05g053860.2.1 
##                  2                  2                  2 
## Solyc05g053910.1.1 Solyc05g054320.2.1 Solyc05g055070.2.1 
##                  2                  2                  2 
## Solyc05g055600.2.1 Solyc06g005330.2.1 Solyc06g007340.2.1 
##                  2                  2                  2 
## Solyc06g007880.1.1 Solyc06g009040.2.1 Solyc06g033870.1.1 
##                  2                  2                  2 
## Solyc06g034130.2.1 Solyc06g035470.1.1 Solyc06g048860.1.1 
##                  2                  2                  2 
## Solyc06g052010.1.1 Solyc06g053420.2.1 Solyc06g053830.2.1 
##                  2                  2                  2 
## Solyc06g054070.2.1 Solyc06g060100.2.1 Solyc06g062840.2.1 
##                  2                  2                  2 
## Solyc06g064710.1.1 Solyc06g065030.2.1 Solyc06g065380.2.1 
##                  2                  2                  2 
## Solyc06g065660.1.1 Solyc06g065670.2.1 Solyc06g066820.2.1 
##                  2                  2                  2 
## Solyc06g068990.2.1 Solyc06g071320.2.1 Solyc06g071410.2.1 
##                  2                  2                  2 
## Solyc06g071700.1.1 Solyc06g072300.2.1 Solyc06g073860.1.1 
##                  2                  2                  2 
## Solyc06g074410.2.1 Solyc06g074790.1.1 Solyc06g075260.2.1 
##                  2                  2                  2 
## Solyc06g075500.2.1 Solyc06g082270.1.1 Solyc06g084380.2.1 
##                  2                  2                  2 
## Solyc07g005770.2.1 Solyc07g006740.2.1 Solyc07g007500.2.1 
##                  2                  2                  2 
## Solyc07g008750.2.1 Solyc07g014580.2.1 Solyc07g042680.2.1 
##                  2                  2                  2 
## Solyc07g047850.2.1 Solyc07g049580.2.1 Solyc07g052020.1.1 
##                  2                  2                  2 
## Solyc07g052430.2.1 Solyc07g052700.2.1 Solyc07g053450.2.1 
##                  2                  2                  2 
## Solyc07g054790.1.1 Solyc07g054820.2.1 Solyc07g056580.2.1 
##                  2                  2                  2 
## Solyc07g063130.2.1 Solyc07g063920.2.1 Solyc07g064810.2.1 
##                  2                  2                  2 
## Solyc08g005410.2.1 Solyc08g006220.2.1 Solyc08g006920.1.1 
##                  2                  2                  2 
## Solyc08g007200.2.1 Solyc08g008030.2.1 Solyc08g014090.1.1 
##                  2                  2                  2 
## Solyc08g014610.2.1 Solyc08g048390.1.1 Solyc08g061570.1.1 
##                  2                  2                  2 
## Solyc08g062450.1.1 Solyc08g062600.1.1 Solyc08g065380.2.1 
##                  2                  2                  2 
## Solyc08g069180.2.1 Solyc08g074550.2.1 Solyc08g075360.1.1 
##                  2                  2                  2 
## Solyc08g076980.2.1 Solyc08g077530.2.1 Solyc08g077560.2.1 
##                  2                  2                  2 
## Solyc08g077960.2.1 Solyc08g078430.2.1 Solyc08g079260.2.1 
##                  2                  2                  2 
## Solyc08g082430.2.1 Solyc09g007310.2.1 Solyc09g009280.1.1 
##                  2                  2                  2 
## Solyc09g009800.2.1 Solyc09g010090.2.1 Solyc09g010680.2.1 
##                  2                  2                  2 
## Solyc09g010990.2.1 Solyc09g011090.1.1 Solyc09g014710.2.1 
##                  2                  2                  2 
## Solyc09g020080.1.1 Solyc09g031600.2.1 Solyc09g031760.1.1 
##                  2                  2                  2 
## Solyc09g059030.2.1 Solyc09g061350.1.1 Solyc09g063030.2.1 
##                  2                  2                  2 
## Solyc09g065930.2.1 Solyc09g074620.2.1 Solyc09g074680.2.1 
##                  2                  2                  2 
## Solyc09g074780.2.1 Solyc09g075450.2.1 Solyc09g082370.2.1 
##                  2                  2                  2 
## Solyc09g082860.2.1 Solyc09g083020.1.1 Solyc09g083310.1.1 
##                  2                  2                  2 
## Solyc09g089580.2.1 Solyc09g090390.1.1 Solyc09g092440.1.1 
##                  2                  2                  2 
## Solyc09g098280.2.1 Solyc10g005330.2.1 Solyc10g005460.2.1 
##                  2                  2                  2 
## Solyc10g007040.2.1 Solyc10g008250.1.1 Solyc10g008440.2.1 
##                  2                  2                  2 
## Solyc10g009050.2.1 Solyc10g009630.1.1 Solyc10g018120.1.1 
##                  2                  2                  2 
## Solyc10g047480.1.1 Solyc10g049950.1.1 Solyc10g050620.1.1 
##                  2                  2                  2 
## Solyc10g051340.1.1 Solyc10g054590.1.1 Solyc10g054900.1.1 
##                  2                  2                  2 
## Solyc10g062340.1.1 Solyc10g074900.1.1 Solyc10g076650.1.1 
##                  2                  2                  2 
## Solyc10g076780.1.1 Solyc10g077000.1.1 Solyc10g077080.1.1 
##                  2                  2                  2 
## Solyc10g079060.1.1 Solyc10g083870.1.1 Solyc10g083970.1.1 
##                  2                  2                  2 
## Solyc10g084150.1.1 Solyc10g084660.1.1 Solyc10g084690.1.1 
##                  2                  2                  2 
## Solyc10g084770.1.1 Solyc10g084860.1.1 Solyc10g085050.1.1 
##                  2                  2                  2 
## Solyc10g086420.1.1 Solyc11g005150.1.1 Solyc11g006230.1.1 
##                  2                  2                  2 
## Solyc11g007380.1.1 Solyc11g010400.1.1 Solyc11g010620.1.1 
##                  2                  2                  2 
## Solyc11g010830.1.1 Solyc11g011670.1.1 Solyc11g011880.1.1 
##                  2                  2                  2 
## Solyc11g012200.1.1 Solyc11g017270.1.1 Solyc11g017300.1.1 
##                  2                  2                  2 
## Solyc11g017400.1.1 Solyc11g021130.1.1 Solyc11g039450.1.1 
##                  2                  2                  2 
## Solyc11g045370.1.1 Solyc11g065660.1.1 Solyc11g066640.1.1 
##                  2                  2                  2 
## Solyc11g066820.1.1 Solyc11g067280.1.1 Solyc11g068670.1.1 
##                  2                  2                  2 
## Solyc11g070140.1.1 Solyc11g071920.1.1 Solyc11g072120.1.1 
##                  2                  2                  2 
## Solyc11g072890.1.1 Solyc12g006690.1.1 Solyc12g009490.1.1 
##                  2                  2                  2 
## Solyc12g010490.1.1 Solyc12g011000.1.1 Solyc12g011140.1.1 
##                  2                  2                  2 
## Solyc12g014250.1.1 Solyc12g014280.1.1 Solyc12g014310.1.1 
##                  2                  2                  2 
## Solyc12g014470.1.1 Solyc12g014560.1.1 Solyc12g019140.1.1 
##                  2                  2                  2 
## Solyc12g019880.1.1 Solyc12g042700.1.1 Solyc12g044440.1.1 
##                  2                  2                  2 
## Solyc12g056080.1.1 Solyc12g056200.1.1 Solyc12g056420.1.1 
##                  2                  2                  2 
## Solyc12g057110.2.1 Solyc12g088390.1.1 Solyc12g088540.1.1 
##                  2                  2                  2 
## Solyc12g088750.1.1 Solyc12g094560.1.1 Solyc12g098330.1.1 
##                  2                  2                  2 
## Solyc12g099980.1.1 Solyc12g099990.1.1 Solyc12g100200.1.1 
##                  2                  2                  2 
## Solyc01g007190.2.1 Solyc01g007500.2.1 Solyc01g007600.2.1 
##                  3                  3                  3 
## Solyc01g007730.2.1 Solyc01g008650.2.1 Solyc01g009450.2.1 
##                  3                  3                  3 
## Solyc01g056960.1.1 Solyc01g057300.1.1 Solyc01g058130.1.1 
##                  3                  3                  3 
## Solyc01g058430.1.1 Solyc01g068020.2.1 Solyc01g068320.1.1 
##                  3                  3                  3 
## Solyc01g079940.2.1 Solyc01g080790.2.1 Solyc01g087480.1.1 
##                  3                  3                  3 
## Solyc01g088690.2.1 Solyc01g091170.2.1 Solyc01g097550.2.1 
##                  3                  3                  3 
## Solyc01g099660.2.1 Solyc01g104820.2.1 Solyc01g106050.2.1 
##                  3                  3                  3 
## Solyc01g106700.2.1 Solyc01g107220.2.1 Solyc01g107880.2.1 
##                  3                  3                  3 
## Solyc01g109270.2.1 Solyc01g109310.2.1 Solyc01g109450.2.1 
##                  3                  3                  3 
## Solyc01g109540.2.1 Solyc01g109800.2.1 Solyc02g014540.1.1 
##                  3                  3                  3 
## Solyc02g030250.2.1 Solyc02g036260.2.1 Solyc02g061980.2.1 
##                  3                  3                  3 
## Solyc02g062340.2.1 Solyc02g062890.1.1 Solyc02g063050.2.1 
##                  3                  3                  3 
## Solyc02g065240.2.1 Solyc02g068930.2.1 Solyc02g069200.1.1 
##                  3                  3                  3 
## Solyc02g071320.2.1 Solyc02g072420.1.1 Solyc02g077160.2.1 
##                  3                  3                  3 
## Solyc02g079310.1.1 Solyc02g082080.1.1 Solyc02g083470.2.1 
##                  3                  3                  3 
## Solyc02g083520.2.1 Solyc02g085750.2.1 Solyc02g085980.1.1 
##                  3                  3                  3 
## Solyc02g089700.2.1 Solyc02g090990.1.1 Solyc02g091520.2.1 
##                  3                  3                  3 
## Solyc02g091630.1.1 Solyc03g005170.2.1 Solyc03g006670.2.1 
##                  3                  3                  3 
## Solyc03g007320.2.1 Solyc03g008010.2.1 Solyc03g020040.2.1 
##                  3                  3                  3 
## Solyc03g025520.2.1 Solyc03g031620.2.1 Solyc03g031780.2.1 
##                  3                  3                  3 
## Solyc03g033710.2.1 Solyc03g034180.2.1 Solyc03g081200.1.1 
##                  3                  3                  3 
## Solyc03g096990.2.1 Solyc03g097080.2.1 Solyc03g097500.2.1 
##                  3                  3                  3 
## Solyc03g112960.1.1 Solyc03g114890.2.1 Solyc03g115410.2.1 
##                  3                  3                  3 
## Solyc03g117850.2.1 Solyc03g118410.2.1 Solyc03g118970.2.1 
##                  3                  3                  3 
## Solyc03g119680.1.1 Solyc03g121540.2.1 Solyc04g005690.2.1 
##                  3                  3                  3 
## Solyc04g008640.2.1 Solyc04g015600.2.1 Solyc04g015610.2.1 
##                  3                  3                  3 
## Solyc04g015980.2.1 Solyc04g016010.2.1 Solyc04g016480.2.1 
##                  3                  3                  3 
## Solyc04g025410.1.1 Solyc04g028430.1.1 Solyc04g047850.1.1 
##                  3                  3                  3 
## Solyc04g072940.2.1 Solyc04g074170.1.1 Solyc04g079250.2.1 
##                  3                  3                  3 
## Solyc04g079980.2.1 Solyc05g005140.2.1 Solyc05g005930.1.1 
##                  3                  3                  3 
## Solyc05g008220.2.1 Solyc05g009590.2.1 Solyc05g018410.1.1 
##                  3                  3                  3 
## Solyc05g025890.1.1 Solyc05g043240.1.1 Solyc05g043390.1.1 
##                  3                  3                  3 
## Solyc05g049870.2.1 Solyc05g050830.1.1 Solyc05g051380.2.1 
##                  3                  3                  3 
## Solyc05g052100.2.1 Solyc05g053330.2.1 Solyc05g053540.2.1 
##                  3                  3                  3 
## Solyc05g054720.2.1 Solyc05g055410.1.1 Solyc05g055690.1.1 
##                  3                  3                  3 
## Solyc05g056200.1.1 Solyc05g056480.2.1 Solyc05g056620.1.1 
##                  3                  3                  3 
## Solyc06g009650.2.1 Solyc06g009750.2.1 Solyc06g034180.1.1 
##                  3                  3                  3 
## Solyc06g036470.1.1 Solyc06g043050.1.1 Solyc06g053520.2.1 
##                  3                  3                  3 
## Solyc06g060330.1.1 Solyc06g060690.2.1 Solyc06g065010.2.1 
##                  3                  3                  3 
## Solyc06g066370.2.1 Solyc06g066760.2.1 Solyc06g073730.1.1 
##                  3                  3                  3 
## Solyc06g075050.1.1 Solyc06g075580.2.1 Solyc06g075900.1.1 
##                  3                  3                  3 
## Solyc06g083020.1.1 Solyc06g083470.2.1 Solyc06g083600.1.1 
##                  3                  3                  3 
## Solyc06g084160.2.1 Solyc07g007150.1.1 Solyc07g009060.2.1 
##                  3                  3                  3 
## Solyc07g009250.1.1 Solyc07g017980.1.1 Solyc07g041030.1.1 
##                  3                  3                  3 
## Solyc07g043050.1.1 Solyc07g047690.1.1 Solyc07g047870.1.1 
##                  3                  3                  3 
## Solyc07g049530.2.1 Solyc07g053910.2.1 Solyc07g054480.1.1 
##                  3                  3                  3 
## Solyc07g055190.2.1 Solyc07g055750.2.1 Solyc07g056660.2.1 
##                  3                  3                  3 
## Solyc07g065520.2.1 Solyc08g005370.1.1 Solyc08g006240.1.1 
##                  3                  3                  3 
## Solyc08g006330.2.1 Solyc08g007860.2.1 Solyc08g013700.1.1 
##                  3                  3                  3 
## Solyc08g022070.2.1 Solyc08g066770.2.1 Solyc08g066790.2.1 
##                  3                  3                  3 
## Solyc08g066800.2.1 Solyc08g068830.2.1 Solyc08g074860.1.1 
##                  3                  3                  3 
## Solyc08g075460.2.1 Solyc08g076320.2.1 Solyc08g076370.2.1 
##                  3                  3                  3 
## Solyc08g076900.2.1 Solyc08g077080.1.1 Solyc08g078270.2.1 
##                  3                  3                  3 
## Solyc08g078850.2.1 Solyc08g080840.1.1 Solyc08g081630.1.1 
##                  3                  3                  3 
## Solyc09g005840.1.1 Solyc09g007550.2.1 Solyc09g007750.2.1 
##                  3                  3                  3 
## Solyc09g009310.1.1 Solyc09g011320.2.1 Solyc09g011520.2.1 
##                  3                  3                  3 
## Solyc09g011550.2.1 Solyc09g011560.2.1 Solyc09g011790.2.1 
##                  3                  3                  3 
## Solyc09g011800.2.1 Solyc09g012020.1.1 Solyc09g014300.2.1 
##                  3                  3                  3 
## Solyc09g015240.1.1 Solyc09g055690.1.1 Solyc09g075060.2.1 
##                  3                  3                  3 
## Solyc09g075430.2.1 Solyc09g083300.1.1 Solyc09g089830.2.1 
##                  3                  3                  3 
## Solyc09g090210.2.1 Solyc10g007200.2.1 Solyc10g007220.1.1 
##                  3                  3                  3 
## Solyc10g008860.1.1 Solyc10g012060.2.1 Solyc10g017810.1.1 
##                  3                  3                  3 
## Solyc10g018530.1.1 Solyc10g045230.1.1 Solyc10g047950.1.1 
##                  3                  3                  3 
## Solyc10g061830.1.1 Solyc10g075100.1.1 Solyc10g076790.1.1 
##                  3                  3                  3 
## Solyc10g079320.1.1 Solyc10g080050.1.1 Solyc10g080100.1.1 
##                  3                  3                  3 
## Solyc10g081130.1.1 Solyc10g083530.1.1 Solyc10g084390.1.1 
##                  3                  3                  3 
## Solyc10g085570.1.1 Solyc10g086780.1.1 Solyc11g005310.1.1 
##                  3                  3                  3 
## Solyc11g008580.1.1 Solyc11g011750.1.1 Solyc11g012560.1.1 
##                  3                  3                  3 
## Solyc11g018550.2.1 Solyc11g020280.1.1 Solyc11g020320.1.1 
##                  3                  3                  3 
## Solyc11g020810.1.1 Solyc11g056540.1.1 Solyc11g062270.1.1 
##                  3                  3                  3 
## Solyc11g067300.1.1 Solyc11g068420.1.1 Solyc11g072390.1.1 
##                  3                  3                  3 
## Solyc12g005250.1.1 Solyc12g006570.1.1 Solyc12g006960.1.1 
##                  3                  3                  3 
## Solyc12g008500.1.1 Solyc12g009820.1.1 Solyc12g010350.1.1 
##                  3                  3                  3 
## Solyc12g010390.1.1 Solyc12g013950.1.1 Solyc12g014490.1.1 
##                  3                  3                  3 
## Solyc12g016220.1.1 Solyc12g019830.1.1 Solyc12g035840.1.1 
##                  3                  3                  3 
## Solyc12g040680.1.1 Solyc12g049030.1.1 Solyc12g056410.1.1 
##                  3                  3                  3 
## Solyc12g062160.1.1 Solyc12g062200.1.1 Solyc12g087920.1.1 
##                  3                  3                  3 
## Solyc12g094460.1.1 Solyc01g005000.2.1 Solyc01g005270.2.1 
##                  3                  4                  4 
## Solyc01g007910.2.1 Solyc01g009400.2.1 Solyc01g014490.2.1 
##                  4                  4                  4 
## Solyc01g058000.2.1 Solyc01g080160.2.1 Solyc01g080390.1.1 
##                  4                  4                  4 
## Solyc01g087260.2.1 Solyc01g087910.2.1 Solyc01g088410.2.1 
##                  4                  4                  4 
## Solyc01g090650.1.1 Solyc01g098030.2.1 Solyc01g100650.2.1 
##                  4                  4                  4 
## Solyc01g105610.1.1 Solyc01g105870.2.1 Solyc01g106350.2.1 
##                  4                  4                  4 
## Solyc02g021260.1.1 Solyc02g030630.1.1 Solyc02g032650.2.1 
##                  4                  4                  4 
## Solyc02g062710.1.1 Solyc02g063190.2.1 Solyc02g070290.2.1 
##                  4                  4                  4 
## Solyc02g070600.1.1 Solyc02g076990.2.1 Solyc02g078990.2.1 
##                  4                  4                  4 
## Solyc02g082300.2.1 Solyc02g082950.2.1 Solyc02g085130.2.1 
##                  4                  4                  4 
## Solyc02g085640.2.1 Solyc02g087180.2.1 Solyc02g087220.2.1 
##                  4                  4                  4 
## Solyc02g088970.1.1 Solyc02g089170.2.1 Solyc02g090030.2.1 
##                  4                  4                  4 
## Solyc02g090050.2.1 Solyc02g092490.2.1 Solyc02g093800.2.1 
##                  4                  4                  4 
## Solyc02g093860.2.1 Solyc03g025760.2.1 Solyc03g026290.2.1 
##                  4                  4                  4 
## Solyc03g034120.2.1 Solyc03g081250.1.1 Solyc03g115370.2.1 
##                  4                  4                  4 
## Solyc03g115470.2.1 Solyc03g118250.2.1 Solyc03g118360.2.1 
##                  4                  4                  4 
## Solyc03g118850.2.1 Solyc03g120390.2.1 Solyc04g007260.2.1 
##                  4                  4                  4 
## Solyc04g008590.2.1 Solyc04g015390.2.1 Solyc04g039620.2.1 
##                  4                  4                  4 
## Solyc04g050390.1.1 Solyc04g050720.2.1 Solyc04g053020.1.1 
##                  4                  4                  4 
## Solyc04g054440.1.1 Solyc04g058180.2.1 Solyc04g071600.2.1 
##                  4                  4                  4 
## Solyc04g076880.2.1 Solyc04g077350.1.1 Solyc04g077370.1.1 
##                  4                  4                  4 
## Solyc04g077390.2.1 Solyc05g006860.2.1 Solyc05g008510.2.1 
##                  4                  4                  4 
## Solyc05g009310.2.1 Solyc05g010320.2.1 Solyc05g015050.2.1 
##                  4                  4                  4 
## Solyc05g026260.1.1 Solyc05g041490.1.1 Solyc05g044540.1.1 
##                  4                  4                  4 
## Solyc05g046060.1.1 Solyc05g047680.2.1 Solyc05g050380.2.1 
##                  4                  4                  4 
## Solyc05g052510.2.1 Solyc05g052910.2.1 Solyc05g053260.2.1 
##                  4                  4                  4 
## Solyc05g053300.2.1 Solyc05g053650.2.1 Solyc05g053820.2.1 
##                  4                  4                  4 
## Solyc05g055680.2.1 Solyc06g005310.2.1 Solyc06g005660.1.1 
##                  4                  4                  4 
## Solyc06g009210.2.1 Solyc06g024360.1.1 Solyc06g036090.1.1 
##                  4                  4                  4 
## Solyc06g050270.1.1 Solyc06g051860.1.1 Solyc06g060180.1.1 
##                  4                  4                  4 
## Solyc06g060270.2.1 Solyc06g060990.2.1 Solyc06g063180.1.1 
##                  4                  4                  4 
## Solyc06g063210.2.1 Solyc06g065450.2.1 Solyc06g071850.2.1 
##                  4                  4                  4 
## Solyc06g072610.2.1 Solyc06g074220.2.1 Solyc06g074650.2.1 
##                  4                  4                  4 
## Solyc06g075450.1.1 Solyc06g075520.2.1 Solyc06g083030.2.1 
##                  4                  4                  4 
## Solyc06g083280.1.1 Solyc06g083520.2.1 Solyc07g005070.1.1 
##                  4                  4                  4 
## Solyc07g006870.2.1 Solyc07g008610.1.1 Solyc07g043480.1.1 
##                  4                  4                  4 
## Solyc07g047760.1.1 Solyc07g053790.1.1 Solyc07g055490.2.1 
##                  4                  4                  4 
## Solyc07g055640.1.1 Solyc07g062400.2.1 Solyc07g064190.1.1 
##                  4                  4                  4 
## Solyc08g006390.1.1 Solyc08g007920.1.1 Solyc08g008010.2.1 
##                  4                  4                  4 
## Solyc08g062720.1.1 Solyc08g067570.1.1 Solyc08g067790.2.1 
##                  4                  4                  4 
## Solyc08g078390.2.1 Solyc08g079230.1.1 Solyc08g080390.2.1 
##                  4                  4                  4 
## Solyc08g080930.1.1 Solyc08g081540.2.1 Solyc08g083390.1.1 
##                  4                  4                  4 
## Solyc09g005670.1.1 Solyc09g007010.1.1 Solyc09g011490.2.1 
##                  4                  4                  4 
## Solyc09g011600.2.1 Solyc09g065560.2.1 Solyc09g074610.2.1 
##                  4                  4                  4 
## Solyc09g075150.2.1 Solyc09g091140.2.1 Solyc09g092390.2.1 
##                  4                  4                  4 
## Solyc09g092470.2.1 Solyc09g098270.2.1 Solyc09g098300.2.1 
##                  4                  4                  4 
## Solyc10g008130.2.1 Solyc10g008510.1.1 Solyc10g009020.2.1 
##                  4                  4                  4 
## Solyc10g036680.1.1 Solyc10g045720.1.1 Solyc10g050410.1.1 
##                  4                  4                  4 
## Solyc10g050970.1.1 Solyc10g052550.1.1 Solyc10g078340.1.1 
##                  4                  4                  4 
## Solyc10g078950.1.1 Solyc10g081180.1.1 Solyc10g085360.1.1 
##                  4                  4                  4 
## Solyc10g086700.1.1 Solyc11g005670.1.1 Solyc11g007830.1.1 
##                  4                  4                  4 
## Solyc11g011300.1.1 Solyc11g011940.1.1 Solyc11g051200.1.1 
##                  4                  4                  4 
## Solyc11g066380.1.1 Solyc11g066910.1.1 Solyc11g067270.1.1 
##                  4                  4                  4 
## Solyc11g070150.1.1 Solyc11g071420.1.1 Solyc11g071740.1.1 
##                  4                  4                  4 
## Solyc12g005590.1.1 Solyc12g009340.1.1 Solyc12g010110.1.1 
##                  4                  4                  4 
## Solyc12g010170.1.1 Solyc12g010540.1.1 Solyc12g013630.1.1 
##                  4                  4                  4 
## Solyc12g017800.1.1 Solyc12g019390.1.1 Solyc12g033040.1.1 
##                  4                  4                  4 
## Solyc12g036810.1.1 Solyc12g040270.1.1 Solyc12g043110.1.1 
##                  4                  4                  4 
## Solyc12g049300.1.1 Solyc12g049350.1.1 Solyc12g049390.1.1 
##                  4                  4                  4 
## Solyc12g056610.1.1 Solyc12g062350.1.1 Solyc12g087870.1.1 
##                  4                  4                  4 
## Solyc12g095830.1.1 Solyc12g095900.1.1 Solyc12g099140.1.1 
##                  4                  4                  4 
## Solyc12g099540.1.1 Solyc01g005580.2.1 Solyc01g005780.1.1 
##                  4                  5                  5 
## Solyc01g006280.2.1 Solyc01g006460.1.1 Solyc01g057910.2.1 
##                  5                  5                  5 
## Solyc01g058320.2.1 Solyc01g079690.2.1 Solyc01g079980.2.1 
##                  5                  5                  5 
## Solyc01g080540.2.1 Solyc01g088100.2.1 Solyc01g088800.2.1 
##                  5                  5                  5 
## Solyc01g091570.2.1 Solyc01g096880.2.1 Solyc01g097750.1.1 
##                  5                  5                  5 
## Solyc01g099050.2.1 Solyc01g103590.2.1 Solyc01g106660.1.1 
##                  5                  5                  5 
## Solyc01g107780.2.1 Solyc01g111810.2.1 Solyc02g021110.1.1 
##                  5                  5                  5 
## Solyc02g036240.1.1 Solyc02g072300.2.1 Solyc02g072400.1.1 
##                  5                  5                  5 
## Solyc02g077100.2.1 Solyc02g083430.1.1 Solyc02g084260.1.1 
##                  5                  5                  5 
## Solyc02g087880.2.1 Solyc02g091460.2.1 Solyc02g092470.2.1 
##                  5                  5                  5 
## Solyc02g093150.2.1 Solyc02g093180.2.1 Solyc03g006950.1.1 
##                  5                  5                  5 
## Solyc03g033500.2.1 Solyc03g034060.2.1 Solyc03g044230.1.1 
##                  5                  5                  5 
## Solyc03g044810.1.1 Solyc03g051940.1.1 Solyc03g082400.2.1 
##                  5                  5                  5 
## Solyc03g093970.2.1 Solyc03g095360.2.1 Solyc03g097320.2.1 
##                  5                  5                  5 
## Solyc03g112010.2.1 Solyc03g121170.2.1 Solyc04g005760.1.1 
##                  5                  5                  5 
## Solyc04g026020.2.1 Solyc04g040120.1.1 Solyc04g047680.1.1 
##                  5                  5                  5 
## Solyc04g052990.1.1 Solyc04g055090.1.1 Solyc04g057860.1.1 
##                  5                  5                  5 
## Solyc04g064590.1.1 Solyc04g076120.2.1 Solyc04g082170.2.1 
##                  5                  5                  5 
## Solyc04g082180.2.1 Solyc05g007710.2.1 Solyc05g008820.2.1 
##                  5                  5                  5 
## Solyc05g011900.1.1 Solyc05g014040.1.1 Solyc05g052390.2.1 
##                  5                  5                  5 
## Solyc05g053030.1.1 Solyc06g008270.2.1 Solyc06g009280.1.1 
##                  5                  5                  5 
## Solyc06g017930.1.1 Solyc06g050300.1.1 Solyc06g054390.2.1 
##                  5                  5                  5 
## Solyc06g054560.2.1 Solyc06g064510.2.1 Solyc06g066200.1.1 
##                  5                  5                  5 
## Solyc06g069100.1.1 Solyc06g071100.2.1 Solyc06g073150.2.1 
##                  5                  5                  5 
## Solyc06g073920.2.1 Solyc06g076890.1.1 Solyc06g083420.1.1 
##                  5                  5                  5 
## Solyc06g083460.2.1 Solyc07g040740.2.1 Solyc07g055840.2.1 
##                  5                  5                  5 
## Solyc08g005200.2.1 Solyc08g006850.2.1 Solyc08g007610.1.1 
##                  5                  5                  5 
## Solyc08g008370.2.1 Solyc08g016010.2.1 Solyc08g048280.1.1 
##                  5                  5                  5 
## Solyc08g066880.2.1 Solyc08g075030.2.1 Solyc08g077950.1.1 
##                  5                  5                  5 
## Solyc08g079160.2.1 Solyc08g079920.1.1 Solyc09g005170.1.1 
##                  5                  5                  5 
## Solyc09g007280.2.1 Solyc09g008520.2.1 Solyc09g009020.2.1 
##                  5                  5                  5 
## Solyc09g009110.2.1 Solyc09g012040.1.1 Solyc09g015800.1.1 
##                  5                  5                  5 
## Solyc09g061760.1.1 Solyc09g064940.2.1 Solyc09g074240.1.1 
##                  5                  5                  5 
## Solyc09g089960.1.1 Solyc09g090420.2.1 Solyc09g092580.2.1 
##                  5                  5                  5 
## Solyc10g005880.2.1 Solyc10g007610.2.1 Solyc10g008480.2.1 
##                  5                  5                  5 
## Solyc10g009090.2.1 Solyc10g018850.1.1 Solyc10g046790.1.1 
##                  5                  5                  5 
## Solyc10g052500.1.1 Solyc10g054040.1.1 Solyc10g054970.1.1 
##                  5                  5                  5 
## Solyc10g079750.1.1 Solyc10g083950.1.1 Solyc10g084280.1.1 
##                  5                  5                  5 
## Solyc11g007220.1.1 Solyc11g008930.1.1 Solyc11g013580.1.1 
##                  5                  5                  5 
## Solyc11g030390.1.1 Solyc11g039980.1.1 Solyc11g056270.1.1 
##                  5                  5                  5 
## Solyc11g062220.1.1 Solyc11g066680.1.1 Solyc11g071700.1.1 
##                  5                  5                  5 
## Solyc11g071760.1.1 Solyc11g072700.1.1 Solyc12g006770.1.1 
##                  5                  5                  5 
## Solyc12g008910.1.1 Solyc12g009450.1.1 Solyc12g009620.1.1 
##                  5                  5                  5 
## Solyc12g014070.1.1 Solyc12g015700.1.1 Solyc12g027740.1.1 
##                  5                  5                  5 
## Solyc12g044340.1.1 Solyc12g044920.1.1 Solyc12g056650.1.1 
##                  5                  5                  5 
## Solyc12g088830.1.1 Solyc12g089180.1.1 Solyc12g096160.1.1 
##                  5                  5                  5 
## Solyc01g006920.2.1 Solyc01g007990.2.1 Solyc01g009630.2.1 
##                  6                  6                  6 
## Solyc01g009890.1.1 Solyc01g010390.2.1 Solyc01g015060.1.1 
##                  6                  6                  6 
## Solyc01g057840.2.1 Solyc01g068070.2.1 Solyc01g090320.2.1 
##                  6                  6                  6 
## Solyc01g098090.2.1 Solyc01g099160.2.1 Solyc01g099310.2.1 
##                  6                  6                  6 
## Solyc01g103250.2.1 Solyc01g105540.2.1 Solyc01g106870.2.1 
##                  6                  6                  6 
## Solyc01g107810.2.1 Solyc01g108540.2.1 Solyc01g109440.2.1 
##                  6                  6                  6 
## Solyc02g038680.1.1 Solyc02g064800.2.1 Solyc02g069210.2.1 
##                  6                  6                  6 
## Solyc02g069250.2.1 Solyc02g070240.2.1 Solyc02g071500.2.1 
##                  6                  6                  6 
## Solyc02g071580.2.1 Solyc02g071610.2.1 Solyc02g071830.1.1 
##                  6                  6                  6 
## Solyc02g072350.1.1 Solyc02g080790.2.1 Solyc03g006030.2.1 
##                  6                  6                  6 
## Solyc03g031450.2.1 Solyc03g032160.2.1 Solyc03g033840.2.1 
##                  6                  6                  6 
## Solyc03g043890.2.1 Solyc03g082430.1.1 Solyc03g123910.2.1 
##                  6                  6                  6 
## Solyc04g006940.2.1 Solyc04g011740.2.1 Solyc04g015080.2.1 
##                  6                  6                  6 
## Solyc04g051350.2.1 Solyc04g074450.1.1 Solyc04g079520.2.1 
##                  6                  6                  6 
## Solyc05g005640.2.1 Solyc05g007350.1.1 Solyc05g008210.2.1 
##                  6                  6                  6 
## Solyc05g018220.1.1 Solyc05g050340.2.1 Solyc05g055260.2.1 
##                  6                  6                  6 
## Solyc06g065790.1.1 Solyc06g069370.2.1 Solyc06g072450.1.1 
##                  6                  6                  6 
## Solyc06g073030.1.1 Solyc06g074840.2.1 Solyc06g074900.1.1 
##                  6                  6                  6 
## Solyc06g075920.1.1 Solyc06g083100.1.1 Solyc06g083960.1.1 
##                  6                  6                  6 
## Solyc07g021050.1.1 Solyc07g021230.1.1 Solyc07g032590.1.1 
##                  6                  6                  6 
## Solyc07g043110.1.1 Solyc07g052770.2.1 Solyc07g056000.2.1 
##                  6                  6                  6 
## Solyc07g061740.2.1 Solyc07g062490.1.1 Solyc07g063400.2.1 
##                  6                  6                  6 
## Solyc07g065500.1.1 Solyc07g065820.2.1 Solyc07g066260.2.1 
##                  6                  6                  6 
## Solyc08g005020.2.1 Solyc08g006860.2.1 Solyc08g007160.2.1 
##                  6                  6                  6 
## Solyc08g014240.2.1 Solyc08g014580.2.1 Solyc08g067000.2.1 
##                  6                  6                  6 
## Solyc08g074630.1.1 Solyc08g076890.2.1 Solyc08g079190.1.1 
##                  6                  6                  6 
## Solyc08g080380.2.1 Solyc09g009510.2.1 Solyc09g010950.2.1 
##                  6                  6                  6 
## Solyc09g011590.2.1 Solyc09g055190.1.1 Solyc09g082870.1.1 
##                  6                  6                  6 
## Solyc09g090190.2.1 Solyc09g090250.2.1 Solyc09g090970.2.1 
##                  6                  6                  6 
## Solyc09g091040.2.1 Solyc09g092760.2.1 Solyc10g006820.2.1 
##                  6                  6                  6 
## Solyc10g047210.1.1 Solyc10g079460.1.1 Solyc10g085030.1.1 
##                  6                  6                  6 
## Solyc10g085630.1.1 Solyc10g085870.1.1 Solyc10g086030.1.1 
##                  6                  6                  6 
## Solyc10g086070.1.1 Solyc11g011740.1.1 Solyc11g012410.1.1 
##                  6                  6                  6 
## Solyc11g065400.1.1 Solyc11g072560.1.1 Solyc11g072720.1.1 
##                  6                  6                  6 
## Solyc12g005340.1.1 Solyc12g006850.1.1 Solyc12g007260.1.1 
##                  6                  6                  6 
## Solyc12g009910.1.1 Solyc12g014630.1.1 Solyc12g056700.1.1 
##                  6                  6                  6 
## Solyc12g096710.1.1 Solyc12g098180.1.1 Solyc12g099740.1.1 
##                  6                  6                  6 
## Solyc01g006580.2.1 Solyc01g007160.2.1 Solyc01g058510.1.1 
##                  7                  7                  7 
## Solyc01g066190.1.1 Solyc01g067520.2.1 Solyc01g094960.2.1 
##                  7                  7                  7 
## Solyc01g097280.2.1 Solyc01g097490.1.1 Solyc01g108570.2.1 
##                  7                  7                  7 
## Solyc02g032590.1.1 Solyc02g066910.2.1 Solyc02g069840.2.1 
##                  7                  7                  7 
## Solyc02g070400.2.1 Solyc02g071860.2.1 Solyc02g079990.2.1 
##                  7                  7                  7 
## Solyc02g081670.1.1 Solyc02g087620.2.1 Solyc02g090860.2.1 
##                  7                  7                  7 
## Solyc03g020080.2.1 Solyc03g032180.2.1 Solyc03g044840.1.1 
##                  7                  7                  7 
## Solyc03g058960.1.1 Solyc03g059180.2.1 Solyc03g082810.1.1 
##                  7                  7                  7 
## Solyc03g098300.1.1 Solyc03g110880.2.1 Solyc03g111130.1.1 
##                  7                  7                  7 
## Solyc03g113960.2.1 Solyc03g122090.2.1 Solyc04g009370.2.1 
##                  7                  7                  7 
## Solyc04g009490.1.1 Solyc04g011440.2.1 Solyc04g052940.1.1 
##                  7                  7                  7 
## Solyc04g081800.1.1 Solyc05g005330.2.1 Solyc05g005950.2.1 
##                  7                  7                  7 
## Solyc05g006640.2.1 Solyc05g050490.2.1 Solyc06g008710.1.1 
##                  7                  7                  7 
## Solyc06g011460.1.1 Solyc06g024240.1.1 Solyc06g036670.1.1 
##                  7                  7                  7 
## Solyc06g052140.1.1 Solyc06g068240.2.1 Solyc06g068650.2.1 
##                  7                  7                  7 
## Solyc06g075270.2.1 Solyc06g083190.2.1 Solyc07g021660.1.1 
##                  7                  7                  7 
## Solyc07g032610.1.1 Solyc07g041550.2.1 Solyc07g054560.1.1 
##                  7                  7                  7 
## Solyc07g056670.2.1 Solyc07g062610.2.1 Solyc07g062910.2.1 
##                  7                  7                  7 
## Solyc07g063770.2.1 Solyc08g005290.2.1 Solyc08g005720.2.1 
##                  7                  7                  7 
## Solyc08g013880.2.1 Solyc08g076620.1.1 Solyc08g079370.1.1 
##                  7                  7                  7 
## Solyc08g080620.1.1 Solyc08g082040.2.1 Solyc09g011480.2.1 
##                  7                  7                  7 
## Solyc09g011540.2.1 Solyc09g014510.2.1 Solyc09g055870.2.1 
##                  7                  7                  7 
## Solyc09g057700.1.1 Solyc09g066410.1.1 Solyc09g075910.1.1 
##                  7                  7                  7 
## Solyc09g091550.2.1 Solyc09g091670.2.1 Solyc10g012180.1.1 
##                  7                  7                  7 
## Solyc10g048120.1.1 Solyc10g051390.1.1 Solyc10g052530.1.1 
##                  7                  7                  7 
## Solyc10g078680.1.1 Solyc11g007850.1.1 Solyc11g012660.1.1 
##                  7                  7                  7 
## Solyc11g039420.1.1 Solyc11g039990.1.1 Solyc11g062130.1.1 
##                  7                  7                  7 
## Solyc11g066670.1.1 Solyc11g072760.1.1 Solyc12g005330.1.1 
##                  7                  7                  7 
## Solyc12g006530.1.1 Solyc12g007070.1.1 Solyc12g009300.1.1 
##                  7                  7                  7 
## Solyc12g035240.1.1 Solyc12g044710.1.1 Solyc12g087900.1.1 
##                  7                  7                  7 
## Solyc12g096410.1.1 Solyc12g096750.1.1 Solyc12g099250.1.1 
##                  7                  7                  7 
## Solyc01g008000.2.1 Solyc01g067870.2.1 Solyc01g094270.2.1 
##                  8                  8                  8 
## Solyc01g096740.2.1 Solyc01g099770.2.1 Solyc01g105150.2.1 
##                  8                  8                  8 
## Solyc02g021620.2.1 Solyc02g070800.2.1 Solyc02g071490.2.1 
##                  8                  8                  8 
## Solyc02g071720.2.1 Solyc02g079510.2.1 Solyc02g081040.2.1 
##                  8                  8                  8 
## Solyc02g081620.2.1 Solyc02g082040.2.1 Solyc02g085220.2.1 
##                  8                  8                  8 
## Solyc02g090350.2.1 Solyc02g091300.2.1 Solyc02g092330.2.1 
##                  8                  8                  8 
## Solyc03g006630.2.1 Solyc03g025470.2.1 Solyc03g033980.2.1 
##                  8                  8                  8 
## Solyc03g078170.1.1 Solyc03g112540.2.1 Solyc03g119120.2.1 
##                  8                  8                  8 
## Solyc03g120990.2.1 Solyc03g121250.2.1 Solyc04g007760.2.1 
##                  8                  8                  8 
## Solyc04g009150.1.1 Solyc04g009910.2.1 Solyc04g011400.2.1 
##                  8                  8                  8 
## Solyc04g011680.1.1 Solyc04g057920.1.1 Solyc04g077270.2.1 
##                  8                  8                  8 
## Solyc05g005920.2.1 Solyc06g008300.2.1 Solyc06g060980.1.1 
##                  8                  8                  8 
## Solyc06g072870.1.1 Solyc06g076710.1.1 Solyc06g082630.2.1 
##                  8                  8                  8 
## Solyc07g005910.2.1 Solyc07g019640.1.1 Solyc07g043680.2.1 
##                  8                  8                  8 
## Solyc07g055000.1.1 Solyc07g056440.2.1 Solyc07g062530.2.1 
##                  8                  8                  8 
## Solyc07g062920.2.1 Solyc08g007730.2.1 Solyc08g041950.1.1 
##                  8                  8                  8 
## Solyc08g044400.1.1 Solyc08g078820.2.1 Solyc08g080650.1.1 
##                  8                  8                  8 
## Solyc09g007760.2.1 Solyc09g009910.2.1 Solyc09g011020.2.1 
##                  8                  8                  8 
## Solyc09g014730.2.1 Solyc09g037150.1.1 Solyc09g047860.1.1 
##                  8                  8                  8 
## Solyc09g065160.2.1 Solyc09g089780.2.1 Solyc10g006700.1.1 
##                  8                  8                  8 
## Solyc10g054170.1.1 Solyc10g074640.1.1 Solyc10g076370.1.1 
##                  8                  8                  8 
## Solyc10g076710.1.1 Solyc10g079570.1.1 Solyc10g079650.1.1 
##                  8                  8                  8 
## Solyc10g080640.1.1 Solyc10g083480.1.1 Solyc10g084940.1.1 
##                  8                  8                  8 
## Solyc11g005320.1.1 Solyc11g013400.1.1 Solyc11g028120.1.1 
##                  8                  8                  8 
## Solyc11g056510.1.1 Solyc11g073200.1.1 Solyc12g055700.1.1 
##                  8                  8                  8 
## Solyc12g094590.1.1 Solyc01g008720.1.1 Solyc01g020520.2.1 
##                  8                  9                  9 
## Solyc01g057260.2.1 Solyc01g087820.2.1 Solyc01g095200.2.1 
##                  9                  9                  9 
## Solyc01g106640.2.1 Solyc01g111250.2.1 Solyc02g005220.1.1 
##                  9                  9                  9 
## Solyc02g068320.2.1 Solyc02g072330.1.1 Solyc02g078280.2.1 
##                  9                  9                  9 
## Solyc02g081820.2.1 Solyc02g082360.2.1 Solyc02g082870.2.1 
##                  9                  9                  9 
## Solyc02g083050.1.1 Solyc02g084770.2.1 Solyc02g085120.2.1 
##                  9                  9                  9 
## Solyc02g085560.2.1 Solyc02g087330.2.1 Solyc03g046370.1.1 
##                  9                  9                  9 
## Solyc03g080090.2.1 Solyc03g083540.2.1 Solyc03g097700.2.1 
##                  9                  9                  9 
## Solyc03g112710.1.1 Solyc04g009350.2.1 Solyc04g010310.2.1 
##                  9                  9                  9 
## Solyc04g025750.2.1 Solyc04g058140.2.1 Solyc04g071160.2.1 
##                  9                  9                  9 
## Solyc04g081390.2.1 Solyc04g082790.2.1 Solyc05g008680.1.1 
##                  9                  9                  9 
## Solyc05g013270.1.1 Solyc05g016230.2.1 Solyc05g023900.1.1 
##                  9                  9                  9 
## Solyc06g043070.2.1 Solyc06g063040.1.1 Solyc06g072000.1.1 
##                  9                  9                  9 
## Solyc06g072080.2.1 Solyc07g017750.2.1 Solyc07g021180.1.1 
##                  9                  9                  9 
## Solyc07g021340.2.1 Solyc07g039550.2.1 Solyc08g007690.1.1 
##                  9                  9                  9 
## Solyc08g029260.1.1 Solyc08g062920.2.1 Solyc08g066660.1.1 
##                  9                  9                  9 
## Solyc08g069060.2.1 Solyc08g079200.1.1 Solyc08g079270.2.1 
##                  9                  9                  9 
## Solyc08g079280.2.1 Solyc09g059040.2.1 Solyc09g065210.2.1 
##                  9                  9                  9 
## Solyc10g012240.2.1 Solyc10g050660.1.1 Solyc10g076240.1.1 
##                  9                  9                  9 
## Solyc10g079340.1.1 Solyc10g085640.1.1 Solyc11g007280.1.1 
##                  9                  9                  9 
## Solyc11g007770.1.1 Solyc11g013210.1.1 Solyc11g013270.1.1 
##                  9                  9                  9 
## Solyc11g018800.1.1 Solyc11g028150.1.1 Solyc11g069710.1.1 
##                  9                  9                  9 
## Solyc11g072110.1.1 Solyc12g006720.1.1 Solyc12g009920.1.1 
##                  9                  9                  9 
## Solyc12g011240.1.1 Solyc12g014000.1.1 Solyc12g039150.1.1 
##                  9                  9                  9 
## Solyc12g040390.1.1 Solyc12g042340.1.1 Solyc12g042680.1.1 
##                  9                  9                  9 
## Solyc12g049190.1.1 Solyc12g056480.1.1 Solyc12g096150.1.1 
##                  9                  9                  9 
## Solyc01g016970.1.1 Solyc01g020440.2.1 Solyc01g056650.1.1 
##                 10                 10                 10 
## Solyc01g060140.2.1 Solyc01g087800.2.1 Solyc01g091350.2.1 
##                 10                 10                 10 
## Solyc01g102990.2.1 Solyc01g105310.2.1 Solyc02g005510.2.1 
##                 10                 10                 10 
## Solyc02g043820.1.1 Solyc02g069260.2.1 Solyc02g070130.1.1 
##                 10                 10                 10 
## Solyc02g071200.2.1 Solyc02g071430.2.1 Solyc02g077430.2.1 
##                 10                 10                 10 
## Solyc02g078610.2.1 Solyc02g079320.2.1 Solyc02g080990.1.1 
##                 10                 10                 10 
## Solyc02g087680.1.1 Solyc02g088650.1.1 Solyc02g093360.2.1 
##                 10                 10                 10 
## Solyc03g007500.2.1 Solyc03g079980.1.1 Solyc03g095210.1.1 
##                 10                 10                 10 
## Solyc03g118720.2.1 Solyc04g009300.2.1 Solyc04g011590.2.1 
##                 10                 10                 10 
## Solyc04g077340.2.1 Solyc05g009880.2.1 Solyc05g050480.1.1 
##                 10                 10                 10 
## Solyc06g043010.1.1 Solyc06g051300.2.1 Solyc06g060410.2.1 
##                 10                 10                 10 
## Solyc06g073960.2.1 Solyc06g075320.2.1 Solyc06g084820.1.1 
##                 10                 10                 10 
## Solyc07g045030.2.1 Solyc07g049660.2.1 Solyc08g048370.2.1 
##                 10                 10                 10 
## Solyc08g067170.1.1 Solyc08g074400.1.1 Solyc08g074650.2.1 
##                 10                 10                 10 
## Solyc08g079870.1.1 Solyc09g011080.2.1 Solyc09g065030.2.1 
##                 10                 10                 10 
## Solyc09g072950.1.1 Solyc09g074450.1.1 Solyc10g006540.2.1 
##                 10                 10                 10 
## Solyc10g047660.1.1 Solyc10g049890.1.1 Solyc10g055800.1.1 
##                 10                 10                 10 
## Solyc10g083350.1.1 Solyc10g084480.1.1 Solyc11g011290.1.1 
##                 10                 10                 10 
## Solyc11g011640.1.1 Solyc11g011960.1.1 Solyc11g020590.1.1 
##                 10                 10                 10 
## Solyc11g066600.1.1 Solyc12g044930.1.1 Solyc12g057060.1.1 
##                 10                 10                 10 
## Solyc12g088460.1.1 Solyc12g089010.1.1 Solyc01g005610.2.1 
##                 10                 10                 11 
## Solyc01g006300.2.1 Solyc01g008440.2.1 Solyc01g008730.2.1 
##                 11                 11                 11 
## Solyc01g010360.2.1 Solyc01g011510.2.1 Solyc01g014990.1.1 
##                 11                 11                 11 
## Solyc01g065740.2.1 Solyc01g068510.1.1 Solyc01g073780.2.1 
##                 11                 11                 11 
## Solyc01g087810.2.1 Solyc01g099020.2.1 Solyc02g036390.1.1 
##                 11                 11                 11 
## Solyc02g062580.2.1 Solyc02g067600.1.1 Solyc02g077000.2.1 
##                 11                 11                 11 
## Solyc02g079330.2.1 Solyc02g086290.1.1 Solyc02g088220.2.1 
##                 11                 11                 11 
## Solyc02g088290.2.1 Solyc02g090690.1.1 Solyc03g082670.2.1 
##                 11                 11                 11 
## Solyc03g093540.1.1 Solyc03g111160.2.1 Solyc03g115430.2.1 
##                 11                 11                 11 
## Solyc03g121210.2.1 Solyc04g014400.2.1 Solyc04g015430.2.1 
##                 11                 11                 11 
## Solyc04g079350.1.1 Solyc04g082430.2.1 Solyc04g082820.2.1 
##                 11                 11                 11 
## Solyc05g005060.2.1 Solyc05g006900.1.1 Solyc05g008070.2.1 
##                 11                 11                 11 
## Solyc05g013320.1.1 Solyc05g021430.1.1 Solyc06g005670.2.1 
##                 11                 11                 11 
## Solyc06g069380.2.1 Solyc06g083850.2.1 Solyc07g008110.2.1 
##                 11                 11                 11 
## Solyc07g017640.2.1 Solyc07g040820.1.1 Solyc07g054230.2.1 
##                 11                 11                 11 
## Solyc07g054370.2.1 Solyc07g056420.2.1 Solyc08g007710.2.1 
##                 11                 11                 11 
## Solyc08g044360.1.1 Solyc08g074410.2.1 Solyc09g007140.2.1 
##                 11                 11                 11 
## Solyc09g009850.2.1 Solyc09g014320.2.1 Solyc09g064270.2.1 
##                 11                 11                 11 
## Solyc09g075390.2.1 Solyc09g089820.1.1 Solyc10g054980.1.1 
##                 11                 11                 11 
## Solyc10g079930.1.1 Solyc11g007870.1.1 Solyc11g013240.1.1 
##                 11                 11                 11 
## Solyc11g017260.1.1 Solyc11g018740.1.1 Solyc11g050860.1.1 
##                 11                 11                 11 
## Solyc11g063540.1.1 Solyc11g072990.1.1 Solyc12g096590.1.1 
##                 11                 11                 11 
## Solyc12g099730.1.1 Solyc01g014530.2.1 Solyc01g091030.2.1 
##                 11                 12                 12 
## Solyc01g094000.2.1 Solyc01g108950.1.1 Solyc01g110570.2.1 
##                 12                 12                 12 
## Solyc02g061660.1.1 Solyc02g063160.2.1 Solyc02g069270.2.1 
##                 12                 12                 12 
## Solyc02g069540.1.1 Solyc02g079710.2.1 Solyc02g082930.2.1 
##                 12                 12                 12 
## Solyc02g087090.2.1 Solyc02g090450.2.1 Solyc03g025360.2.1 
##                 12                 12                 12 
## Solyc03g032110.1.1 Solyc03g094150.1.1 Solyc03g111530.2.1 
##                 12                 12                 12 
## Solyc03g112970.1.1 Solyc04g011940.1.1 Solyc04g050070.1.1 
##                 12                 12                 12 
## Solyc04g076630.2.1 Solyc05g018120.1.1 Solyc05g050470.1.1 
##                 12                 12                 12 
## Solyc05g053360.2.1 Solyc06g062680.1.1 Solyc07g006450.1.1 
##                 12                 12                 12 
## Solyc07g017930.1.1 Solyc07g045090.2.1 Solyc07g049120.1.1 
##                 12                 12                 12 
## Solyc07g052400.2.1 Solyc08g005770.2.1 Solyc08g007300.1.1 
##                 12                 12                 12 
## Solyc08g007310.2.1 Solyc08g014330.2.1 Solyc08g065460.1.1 
##                 12                 12                 12 
## Solyc08g075240.2.1 Solyc08g075610.1.1 Solyc08g078800.1.1 
##                 12                 12                 12 
## Solyc09g010550.2.1 Solyc09g090870.2.1 Solyc10g009290.1.1 
##                 12                 12                 12 
## Solyc10g047680.1.1 Solyc10g052510.1.1 Solyc10g078860.1.1 
##                 12                 12                 12 
## Solyc10g084490.1.1 Solyc10g086220.1.1 Solyc10g086600.1.1 
##                 12                 12                 12 
## Solyc11g044610.1.1 Solyc11g066590.1.1 Solyc12g006590.1.1 
##                 12                 12                 12 
## Solyc12g017660.1.1 Solyc12g056300.1.1 Solyc01g006540.2.1 
##                 12                 12                 13 
## Solyc01g079970.2.1 Solyc01g080570.2.1 Solyc01g080660.2.1 
##                 13                 13                 13 
## Solyc01g090610.2.1 Solyc01g094530.2.1 Solyc01g099190.2.1 
##                 13                 13                 13 
## Solyc02g061610.1.1 Solyc02g080850.1.1 Solyc02g085650.2.1 
##                 13                 13                 13 
## Solyc03g007570.2.1 Solyc03g033900.1.1 Solyc03g062910.2.1 
##                 13                 13                 13 
## Solyc03g082450.2.1 Solyc03g098530.1.1 Solyc03g115350.1.1 
##                 13                 13                 13 
## Solyc04g005540.2.1 Solyc04g010020.2.1 Solyc04g024690.1.1 
##                 13                 13                 13 
## Solyc04g054740.2.1 Solyc04g076160.1.1 Solyc04g080760.2.1 
##                 13                 13                 13 
## Solyc05g005800.2.1 Solyc05g009140.2.1 Solyc05g054330.2.1 
##                 13                 13                 13 
## Solyc05g056050.2.1 Solyc06g005290.2.1 Solyc06g065070.1.1 
##                 13                 13                 13 
## Solyc06g082760.2.1 Solyc06g084060.2.1 Solyc07g055180.2.1 
##                 13                 13                 13 
## Solyc08g006520.1.1 Solyc08g008430.2.1 Solyc08g015730.1.1 
##                 13                 13                 13 
## Solyc08g015750.1.1 Solyc08g028940.1.1 Solyc08g042130.2.1 
##                 13                 13                 13 
## Solyc09g008110.1.1 Solyc09g011010.2.1 Solyc09g018070.1.1 
##                 13                 13                 13 
## Solyc10g006620.1.1 Solyc10g038140.1.1 Solyc10g079030.1.1 
##                 13                 13                 13 
## Solyc10g079180.2.1 Solyc10g080790.1.1 Solyc10g081980.1.1 
##                 13                 13                 13 
## Solyc11g013700.1.1 Solyc11g019860.1.1 Solyc11g028100.1.1 
##                 13                 13                 13 
## Solyc12g010020.1.1 Solyc01g066420.2.1 Solyc01g081430.2.1 
##                 13                 14                 14 
## Solyc01g096350.2.1 Solyc01g106820.2.1 Solyc01g107830.2.1 
##                 14                 14                 14 
## Solyc01g111940.2.1 Solyc02g030210.2.1 Solyc02g080760.1.1 
##                 14                 14                 14 
## Solyc02g090650.2.1 Solyc02g091210.1.1 Solyc03g006430.2.1 
##                 14                 14                 14 
## Solyc03g006700.2.1 Solyc03g122120.2.1 Solyc04g007180.1.1 
##                 14                 14                 14 
## Solyc05g009470.2.1 Solyc06g072230.1.1 Solyc06g073680.2.1 
##                 14                 14                 14 
## Solyc07g005450.2.1 Solyc07g055480.1.1 Solyc07g063330.2.1 
##                 14                 14                 14 
## Solyc08g007620.1.1 Solyc08g029380.1.1 Solyc08g074940.2.1 
##                 14                 14                 14 
## Solyc09g005460.1.1 Solyc09g011500.2.1 Solyc09g031580.2.1 
##                 14                 14                 14 
## Solyc09g065950.2.1 Solyc10g008230.1.1 Solyc10g009440.2.1 
##                 14                 14                 14 
## Solyc10g047270.1.1 Solyc10g074970.1.1 Solyc10g080930.1.1 
##                 14                 14                 14 
## Solyc11g006520.1.1 Solyc11g011580.1.1 Solyc11g018770.1.1 
##                 14                 14                 14 
## Solyc12g009790.1.1 Solyc12g027870.1.1 Solyc12g044940.1.1 
##                 14                 14                 14 
## Solyc12g100250.1.1 Solyc01g049680.2.1 Solyc01g067700.2.1 
##                 14                 15                 15 
## Solyc01g105660.2.1 Solyc01g109810.2.1 Solyc02g050140.2.1 
##                 15                 15                 15 
## Solyc02g061850.2.1 Solyc02g085720.1.1 Solyc02g088230.2.1 
##                 15                 15                 15 
## Solyc03g025410.2.1 Solyc03g034430.1.1 Solyc03g111030.2.1 
##                 15                 15                 15 
## Solyc04g051170.1.1 Solyc04g072260.1.1 Solyc05g015800.2.1 
##                 15                 15                 15 
## Solyc05g046150.2.1 Solyc05g046190.1.1 Solyc05g051910.1.1 
##                 15                 15                 15 
## Solyc05g053810.2.1 Solyc06g083910.2.1 Solyc07g007600.2.1 
##                 15                 15                 15 
## Solyc07g062350.1.1 Solyc08g014380.1.1 Solyc08g048470.1.1 
##                 15                 15                 15 
## Solyc08g065540.2.1 Solyc08g066190.1.1 Solyc08g080640.1.1 
##                 15                 15                 15 
## Solyc08g080760.1.1 Solyc09g008760.1.1 Solyc09g010040.1.1 
##                 15                 15                 15 
## Solyc09g065510.2.1 Solyc09g089490.2.1 Solyc09g091160.1.1 
##                 15                 15                 15 
## Solyc10g007420.2.1 Solyc10g044480.1.1 Solyc10g086430.1.1 
##                 15                 15                 15 
## Solyc11g006590.1.1 Solyc11g015900.1.1 Solyc11g027630.1.1 
##                 15                 15                 15 
## Solyc12g005440.1.1 Solyc12g099010.1.1 Solyc01g102400.2.1 
##                 15                 15                 16 
## Solyc01g103860.2.1 Solyc01g107940.2.1 Solyc02g014520.2.1 
##                 16                 16                 16 
## Solyc02g032860.2.1 Solyc02g065090.2.1 Solyc02g072310.2.1 
##                 16                 16                 16 
## Solyc02g077250.2.1 Solyc03g058260.1.1 Solyc03g082580.2.1 
##                 16                 16                 16 
## Solyc03g093130.2.1 Solyc03g110900.2.1 Solyc03g115230.2.1 
##                 16                 16                 16 
## Solyc03g122360.2.1 Solyc04g014870.2.1 Solyc04g079240.2.1 
##                 16                 16                 16 
## Solyc05g023780.1.1 Solyc06g052090.1.1 Solyc06g083050.2.1 
##                 16                 16                 16 
## Solyc07g005400.2.1 Solyc07g014690.2.1 Solyc07g017260.2.1 
##                 16                 16                 16 
## Solyc07g054590.1.1 Solyc08g061160.1.1 Solyc08g067450.1.1 
##                 16                 16                 16 
## Solyc09g007870.2.1 Solyc09g014860.2.1 Solyc09g061530.1.1 
##                 16                 16                 16 
## Solyc09g064960.1.1 Solyc09g089510.2.1 Solyc10g050750.1.1 
##                 16                 16                 16 
## Solyc10g061840.1.1 Solyc10g076330.1.1 Solyc10g086740.1.1 
##                 16                 16                 16 
## Solyc11g013740.1.1 Solyc11g071990.1.1 Solyc11g073150.1.1 
##                 16                 16                 16 
## Solyc12g056070.1.1 Solyc01g066610.2.1 Solyc01g099500.1.1 
##                 16                 17                 17 
## Solyc01g100950.2.1 Solyc01g110380.2.1 Solyc02g014030.1.1 
##                 17                 17                 17 
## Solyc02g064900.1.1 Solyc02g067640.2.1 Solyc02g070070.1.1 
##                 17                 17                 17 
## Solyc02g070230.1.1 Solyc02g073580.1.1 Solyc02g083740.1.1 
##                 17                 17                 17 
## Solyc02g084780.2.1 Solyc02g091020.1.1 Solyc03g025230.2.1 
##                 17                 17                 17 
## Solyc03g063040.2.1 Solyc03g111760.2.1 Solyc04g008910.1.1 
##                 17                 17                 17 
## Solyc04g050690.1.1 Solyc04g051830.2.1 Solyc04g071780.2.1 
##                 17                 17                 17 
## Solyc05g006730.2.1 Solyc05g023660.1.1 Solyc05g033910.1.1 
##                 17                 17                 17 
## Solyc06g005160.2.1 Solyc06g024290.1.1 Solyc07g006680.1.1 
##                 17                 17                 17 
## Solyc07g055350.2.1 Solyc08g005080.1.1 Solyc08g005240.1.1 
##                 17                 17                 17 
## Solyc08g007060.2.1 Solyc08g007360.2.1 Solyc08g007670.1.1 
##                 17                 17                 17 
## Solyc08g007900.1.1 Solyc08g013690.1.1 Solyc08g079430.2.1 
##                 17                 17                 17 
## Solyc09g056240.1.1 Solyc10g005260.2.1 Solyc10g012270.1.1 
##                 17                 17                 17 
## Solyc10g051350.1.1 Solyc10g085370.1.1 Solyc10g085460.1.1 
##                 17                 17                 17 
## Solyc11g011920.1.1 Solyc11g045570.1.1 Solyc11g064750.1.1 
##                 17                 17                 17 
## Solyc11g068950.1.1 Solyc12g035290.1.1 Solyc12g056870.1.1 
##                 17                 17                 17 
## Solyc12g088710.1.1 Solyc01g066330.1.1 Solyc01g079960.2.1 
##                 17                 18                 18 
## Solyc01g100860.2.1 Solyc01g104700.2.1 Solyc02g038670.1.1 
##                 18                 18                 18 
## Solyc02g065480.2.1 Solyc02g083000.1.1 Solyc03g019800.2.1 
##                 18                 18                 18 
## Solyc03g111920.1.1 Solyc04g008970.2.1 Solyc04g010000.2.1 
##                 18                 18                 18 
## Solyc04g025170.2.1 Solyc05g007610.2.1 Solyc05g010180.2.1 
##                 18                 18                 18 
## Solyc05g017900.2.1 Solyc05g054350.2.1 Solyc06g066830.2.1 
##                 18                 18                 18 
## Solyc06g076930.1.1 Solyc06g083890.2.1 Solyc07g006730.2.1 
##                 18                 18                 18 
## Solyc07g062480.1.1 Solyc08g016280.1.1 Solyc08g016710.1.1 
##                 18                 18                 18 
## Solyc08g069080.2.1 Solyc08g074830.2.1 Solyc08g080010.1.1 
##                 18                 18                 18 
## Solyc09g014550.2.1 Solyc09g064560.1.1 Solyc12g043120.1.1 
##                 18                 18                 18 
## Solyc12g044520.1.1 Solyc12g049510.1.1 Solyc12g055890.1.1 
##                 18                 18                 18 
## Solyc12g056530.1.1 Solyc12g088250.1.1 Solyc01g067860.2.1 
##                 18                 18                 19 
## Solyc01g090630.2.1 Solyc01g102710.2.1 Solyc01g105770.2.1 
##                 19                 19                 19 
## Solyc02g080310.2.1 Solyc02g084250.2.1 Solyc03g062840.1.1 
##                 19                 19                 19 
## Solyc03g082970.2.1 Solyc03g111970.2.1 Solyc03g120840.1.1 
##                 19                 19                 19 
## Solyc04g056680.1.1 Solyc04g074850.2.1 Solyc05g025920.2.1 
##                 19                 19                 19 
## Solyc05g052110.2.1 Solyc06g051920.2.1 Solyc06g075760.1.1 
##                 19                 19                 19 
## Solyc06g083040.2.1 Solyc07g015980.2.1 Solyc07g054390.1.1 
##                 19                 19                 19 
## Solyc08g005330.1.1 Solyc08g007790.2.1 Solyc08g068710.1.1 
##                 19                 19                 19 
## Solyc08g077740.1.1 Solyc08g082150.1.1 Solyc08g082490.1.1 
##                 19                 19                 19 
## Solyc08g082640.2.1 Solyc09g061750.1.1 Solyc10g076210.1.1 
##                 19                 19                 19 
## Solyc10g085650.1.1 Solyc11g013390.1.1 Solyc11g070090.1.1 
##                 19                 19                 19 
## Solyc11g073250.1.1 Solyc12g017820.1.1 Solyc12g044410.1.1 
##                 19                 19                 19 
## Solyc01g049610.1.1 Solyc01g091160.2.1 Solyc01g096780.2.1 
##                 20                 20                 20 
## Solyc01g104210.2.1 Solyc01g106670.1.1 Solyc02g037620.1.1 
##                 20                 20                 20 
## Solyc02g076660.2.1 Solyc02g083550.1.1 Solyc02g089690.2.1 
##                 20                 20                 20 
## Solyc02g090770.1.1 Solyc03g095390.1.1 Solyc03g095710.2.1 
##                 20                 20                 20 
## Solyc03g096250.2.1 Solyc03g115520.2.1 Solyc04g011760.2.1 
##                 20                 20                 20 
## Solyc04g074660.1.1 Solyc04g077940.2.1 Solyc05g006010.2.1 
##                 20                 20                 20 
## Solyc05g053610.2.1 Solyc08g075490.2.1 Solyc08g079910.1.1 
##                 20                 20                 20 
## Solyc09g066400.1.1 Solyc09g075710.1.1 Solyc09g089730.2.1 
##                 20                 20                 20 
## Solyc10g045400.1.1 Solyc10g049530.1.1 Solyc10g079310.1.1 
##                 20                 20                 20 
## Solyc10g079700.1.1 Solyc10g080320.1.1 Solyc10g086080.1.1 
##                 20                 20                 20 
## Solyc11g062100.1.1 Solyc11g068590.1.1 Solyc11g072460.1.1 
##                 20                 20                 20 
## Solyc12g100030.1.1 Solyc01g008500.2.1 Solyc01g073810.2.1 
##                 20                 21                 21 
## Solyc01g096580.2.1 Solyc01g105690.2.1 Solyc02g071000.1.1 
##                 21                 21                 21 
## Solyc02g071090.2.1 Solyc02g081870.2.1 Solyc02g082180.2.1 
##                 21                 21                 21 
## Solyc02g090260.1.1 Solyc02g094570.2.1 Solyc03g096140.1.1 
##                 21                 21                 21 
## Solyc03g118220.1.1 Solyc04g008330.1.1 Solyc04g064470.1.1 
##                 21                 21                 21 
## Solyc04g082920.2.1 Solyc05g005940.2.1 Solyc05g006000.2.1 
##                 21                 21                 21 
## Solyc05g007290.1.1 Solyc05g014800.1.1 Solyc05g050640.1.1 
##                 21                 21                 21 
## Solyc07g053240.2.1 Solyc08g014230.2.1 Solyc08g065350.2.1 
##                 21                 21                 21 
## Solyc08g068700.1.1 Solyc08g081670.1.1 Solyc09g007120.2.1 
##                 21                 21                 21 
## Solyc09g014240.2.1 Solyc10g007060.2.1 Solyc10g050950.1.1 
##                 21                 21                 21 
## Solyc10g054840.1.1 Solyc10g076200.1.1 Solyc10g078290.1.1 
##                 21                 21                 21 
## Solyc10g080430.1.1 Solyc11g005280.1.1 Solyc11g011840.1.1 
##                 21                 21                 21 
## Solyc11g020060.1.1 Solyc12g094700.1.1 Solyc01g007590.2.1 
##                 21                 21                 22 
## Solyc01g010050.2.1 Solyc01g098670.1.1 Solyc01g099180.2.1 
##                 22                 22                 22 
## Solyc02g070890.2.1 Solyc03g033830.2.1 Solyc04g014740.1.1 
##                 22                 22                 22 
## Solyc04g054250.2.1 Solyc05g012320.1.1 Solyc05g013010.2.1 
##                 22                 22                 22 
## Solyc06g008660.2.1 Solyc06g051410.2.1 Solyc06g062900.2.1 
##                 22                 22                 22 
## Solyc06g073800.2.1 Solyc07g055470.2.1 Solyc08g007340.2.1 
##                 22                 22                 22 
## Solyc08g047940.1.1 Solyc08g079890.1.1 Solyc08g081410.2.1 
##                 22                 22                 22 
## Solyc09g005080.1.1 Solyc09g010800.2.1 Solyc09g098130.1.1 
##                 22                 22                 22 
## Solyc10g006170.2.1 Solyc10g011660.2.1 Solyc10g018870.1.1 
##                 22                 22                 22 
## Solyc10g083690.2.1 Solyc10g085530.1.1 Solyc11g008110.1.1 
##                 22                 22                 22 
## Solyc12g016170.1.1 Solyc12g044820.1.1 Solyc01g005260.2.1 
##                 22                 22                 23 
## Solyc01g009580.1.1 Solyc01g080080.2.1 Solyc01g088120.1.1 
##                 23                 23                 23 
## Solyc01g098950.1.1 Solyc01g106360.2.1 Solyc01g110220.1.1 
##                 23                 23                 23 
## Solyc02g032340.1.1 Solyc02g063090.2.1 Solyc02g068310.2.1 
##                 23                 23                 23 
## Solyc02g069280.2.1 Solyc02g080080.2.1 Solyc03g025220.2.1 
##                 23                 23                 23 
## Solyc03g034110.2.1 Solyc03g059000.1.1 Solyc03g112820.2.1 
##                 23                 23                 23 
## Solyc03g118020.2.1 Solyc04g071070.2.1 Solyc04g074910.2.1 
##                 23                 23                 23 
## Solyc05g008720.1.1 Solyc05g012640.2.1 Solyc05g013470.2.1 
##                 23                 23                 23 
## Solyc05g046020.2.1 Solyc06g034260.1.1 Solyc06g054440.2.1 
##                 23                 23                 23 
## Solyc06g062530.2.1 Solyc06g076200.1.1 Solyc07g063450.1.1 
##                 23                 23                 23 
## Solyc07g064910.2.1 Solyc07g065570.1.1 Solyc08g048450.2.1 
##                 23                 23                 23 
## Solyc08g080670.1.1 Solyc08g080770.2.1 Solyc09g011270.2.1 
##                 23                 23                 23 
## Solyc09g089720.1.1 Solyc09g089860.2.1 Solyc09g098540.2.1 
##                 23                 23                 23 
## Solyc11g062310.1.1 Solyc12g007180.1.1 Solyc12g007250.1.1 
##                 23                 23                 23 
## Solyc12g009540.1.1 Solyc12g089030.1.1 Solyc12g100180.1.1 
##                 23                 23                 23 
## Solyc01g014960.1.1 Solyc01g095120.2.1 Solyc01g098120.2.1 
##                 24                 24                 24 
## Solyc02g021070.1.1 Solyc02g050200.1.1 Solyc02g065330.1.1 
##                 24                 24                 24 
## Solyc02g086210.2.1 Solyc03g083700.1.1 Solyc03g097580.2.1 
##                 24                 24                 24 
## Solyc04g005160.1.1 Solyc04g018100.2.1 Solyc04g050270.1.1 
##                 24                 24                 24 
## Solyc04g074440.1.1 Solyc04g082260.2.1 Solyc05g011890.1.1 
##                 24                 24                 24 
## Solyc05g050070.1.1 Solyc06g005150.2.1 Solyc06g009490.2.1 
##                 24                 24                 24 
## Solyc06g033920.1.1 Solyc06g054620.2.1 Solyc06g059780.1.1 
##                 24                 24                 24 
## Solyc07g018240.1.1 Solyc07g042700.2.1 Solyc07g049780.1.1 
##                 24                 24                 24 
## Solyc08g079980.1.1 Solyc09g061390.1.1 Solyc09g074290.1.1 
##                 24                 24                 24 
## Solyc10g007700.2.1 Solyc10g037900.1.1 Solyc11g028090.1.1 
##                 24                 24                 24 
## Solyc12g006020.1.1 Solyc01g006560.2.1 Solyc01g066950.1.1 
##                 24                 25                 25 
## Solyc01g095840.1.1 Solyc01g099460.1.1 Solyc01g102910.2.1 
##                 25                 25                 25 
## Solyc02g005450.1.1 Solyc02g011800.1.1 Solyc02g079470.1.1 
##                 25                 25                 25 
## Solyc03g005770.1.1 Solyc03g045140.2.1 Solyc03g058470.1.1 
##                 25                 25                 25 
## Solyc03g093560.1.1 Solyc03g094060.2.1 Solyc03g095750.1.1 
##                 25                 25                 25 
## Solyc03g114560.2.1 Solyc04g015400.2.1 Solyc04g079260.2.1 
##                 25                 25                 25 
## Solyc05g013260.1.1 Solyc05g051370.2.1 Solyc06g083090.2.1 
##                 25                 25                 25 
## Solyc07g005620.2.1 Solyc07g008350.2.1 Solyc07g054600.2.1 
##                 25                 25                 25 
## Solyc08g074290.2.1 Solyc08g074360.2.1 Solyc08g079860.1.1 
##                 25                 25                 25 
## Solyc08g079880.1.1 Solyc09g009460.2.1 Solyc11g030710.1.1 
##                 25                 25                 25 
## Solyc11g073260.1.1 Solyc12g088470.1.1 Solyc12g095960.1.1 
##                 25                 25                 25 
## Solyc01g017050.1.1 Solyc01g050010.2.1 Solyc01g099580.1.1 
##                 26                 26                 26 
## Solyc01g100770.2.1 Solyc01g106830.2.1 Solyc02g062060.1.1 
##                 26                 26                 26 
## Solyc02g062130.2.1 Solyc02g065220.2.1 Solyc02g071920.2.1 
##                 26                 26                 26 
## Solyc02g080290.2.1 Solyc02g088170.1.1 Solyc03g083850.1.1 
##                 26                 26                 26 
## Solyc03g111140.2.1 Solyc03g117410.2.1 Solyc04g007330.1.1 
##                 26                 26                 26 
## Solyc05g012740.1.1 Solyc05g013850.2.1 Solyc05g047510.1.1 
##                 26                 26                 26 
## Solyc06g048960.2.1 Solyc06g064500.2.1 Solyc07g052730.2.1 
##                 26                 26                 26 
## Solyc08g014420.2.1 Solyc08g068370.2.1 Solyc08g081040.2.1 
##                 26                 26                 26 
## Solyc09g009670.2.1 Solyc10g017710.1.1 Solyc10g037950.1.1 
##                 26                 26                 26 
## Solyc10g048000.1.1 Solyc10g049270.1.1 Solyc10g061970.1.1 
##                 26                 26                 26 
## Solyc01g008280.2.1 Solyc01g011430.2.1 Solyc01g080360.2.1 
##                 27                 27                 27 
## Solyc01g104540.2.1 Solyc02g065280.2.1 Solyc02g069140.1.1 
##                 27                 27                 27 
## Solyc02g085110.2.1 Solyc02g086510.2.1 Solyc02g090790.1.1 
##                 27                 27                 27 
## Solyc02g091170.2.1 Solyc03g082830.1.1 Solyc04g011840.1.1 
##                 27                 27                 27 
## Solyc04g016550.2.1 Solyc04g064440.1.1 Solyc04g064800.2.1 
##                 27                 27                 27 
## Solyc04g077900.1.1 Solyc04g078150.2.1 Solyc05g018570.2.1 
##                 27                 27                 27 
## Solyc06g054050.1.1 Solyc06g073760.2.1 Solyc08g061920.1.1 
##                 27                 27                 27 
## Solyc08g067610.2.1 Solyc08g074610.1.1 Solyc09g075400.2.1 
##                 27                 27                 27 
## Solyc12g019320.1.1 Solyc01g009270.1.1 Solyc01g056430.1.1 
##                 27                 28                 28 
## Solyc01g058590.1.1 Solyc01g108580.2.1 Solyc01g110950.2.1 
##                 28                 28                 28 
## Solyc02g030540.1.1 Solyc02g077020.2.1 Solyc02g078970.2.1 
##                 28                 28                 28 
## Solyc02g080830.1.1 Solyc02g090930.2.1 Solyc03g062670.1.1 
##                 28                 28                 28 
## Solyc03g097790.2.1 Solyc04g017710.2.1 Solyc04g063370.1.1 
##                 28                 28                 28 
## Solyc05g023950.1.1 Solyc06g030530.2.1 Solyc06g036580.2.1 
##                 28                 28                 28 
## Solyc06g071040.2.1 Solyc06g074990.1.1 Solyc06g075730.1.1 
##                 28                 28                 28 
## Solyc08g022170.1.1 Solyc08g066240.2.1 Solyc08g082810.2.1 
##                 28                 28                 28 
## Solyc09g018060.2.1 Solyc09g066310.2.1 Solyc10g005270.1.1 
##                 28                 28                 28 
## Solyc11g013620.1.1 Solyc11g040290.1.1 Solyc12g019080.1.1 
##                 28                 28                 28 
## Solyc12g056020.1.1 Solyc01g008190.2.1 Solyc01g058190.2.1 
##                 28                 29                 29 
## Solyc01g066890.1.1 Solyc01g087950.2.1 Solyc01g103340.2.1 
##                 29                 29                 29 
## Solyc01g108880.2.1 Solyc02g032430.1.1 Solyc02g070650.2.1 
##                 29                 29                 29 
## Solyc02g079450.1.1 Solyc03g006980.2.1 Solyc03g063960.1.1 
##                 29                 29                 29 
## Solyc03g097940.2.1 Solyc04g012080.1.1 Solyc04g024800.1.1 
##                 29                 29                 29 
## Solyc04g077650.2.1 Solyc06g064700.1.1 Solyc07g015930.1.1 
##                 29                 29                 29 
## Solyc07g025520.2.1 Solyc08g074680.2.1 Solyc08g076570.2.1 
##                 29                 29                 29 
## Solyc08g081960.1.1 Solyc09g065800.2.1 Solyc10g024320.1.1 
##                 29                 29                 29 
## Solyc11g067230.1.1 Solyc11g071970.1.1 Solyc01g009740.1.1 
##                 29                 29                 30 
## Solyc01g080300.2.1 Solyc01g087850.2.1 Solyc01g107720.2.1 
##                 30                 30                 30 
## Solyc02g078150.2.1 Solyc02g088850.2.1 Solyc03g025210.2.1 
##                 30                 30                 30 
## Solyc03g093710.1.1 Solyc03g113940.2.1 Solyc04g007420.2.1 
##                 30                 30                 30 
## Solyc04g011790.1.1 Solyc05g008040.2.1 Solyc05g047700.1.1 
##                 30                 30                 30 
## Solyc06g008450.2.1 Solyc06g048790.1.1 Solyc07g007880.1.1 
##                 30                 30                 30 
## Solyc07g043710.2.1 Solyc07g056480.2.1 Solyc08g078960.2.1 
##                 30                 30                 30 
## Solyc09g010830.2.1 Solyc09g015140.2.1 Solyc10g044750.1.1 
##                 30                 30                 30 
## Solyc10g078880.1.1 Solyc12g040550.1.1 Solyc01g009110.2.1 
##                 30                 30                 31 
## Solyc02g082540.2.1 Solyc03g026310.2.1 Solyc04g058000.1.1 
##                 31                 31                 31 
## Solyc05g042010.1.1 Solyc05g050170.1.1 Solyc06g084180.2.1 
##                 31                 31                 31 
## Solyc08g062540.1.1 Solyc09g074190.1.1 Solyc09g074200.1.1 
##                 31                 31                 31 
## Solyc10g007370.1.1 Solyc10g008680.1.1 Solyc11g067240.1.1 
##                 31                 31                 31 
## Solyc12g005430.1.1 Solyc12g009370.1.1 Solyc12g036470.1.1 
##                 31                 31                 31 
## Solyc01g097220.1.1 Solyc02g062410.1.1 Solyc02g062500.2.1 
##                 32                 32                 32 
## Solyc02g065700.2.1 Solyc02g071670.2.1 Solyc02g083350.2.1 
##                 32                 32                 32 
## Solyc02g091220.1.1 Solyc03g006940.1.1 Solyc03g026190.2.1 
##                 32                 32                 32 
## Solyc03g034020.2.1 Solyc04g049670.2.1 Solyc04g074340.2.1 
##                 32                 32                 32 
## Solyc05g009070.2.1 Solyc05g012650.2.1 Solyc05g013790.2.1 
##                 32                 32                 32 
## Solyc05g054650.1.1 Solyc06g076560.1.1 Solyc07g051980.1.1 
##                 32                 32                 32 
## Solyc07g054770.1.1 Solyc08g005280.1.1 Solyc08g008190.2.1 
##                 32                 32                 32 
## Solyc09g005380.1.1 Solyc09g014580.2.1 Solyc10g055510.1.1 
##                 32                 32                 32 
## Solyc12g088500.1.1 Solyc01g014850.2.1 Solyc01g033990.1.1 
##                 32                 33                 33 
## Solyc01g098350.2.1 Solyc02g005460.1.1 Solyc02g076950.2.1 
##                 33                 33                 33 
## Solyc03g043830.1.1 Solyc03g093490.2.1 Solyc03g116930.2.1 
##                 33                 33                 33 
## Solyc04g079470.2.1 Solyc05g041610.1.1 Solyc06g065990.1.1 
##                 33                 33                 33 
## Solyc07g017290.2.1 Solyc07g061720.2.1 Solyc08g005640.2.1 
##                 33                 33                 33 
## Solyc10g054820.1.1 Solyc11g045050.1.1 Solyc12g006470.1.1 
##                 33                 33                 33 
## Solyc12g099030.1.1 Solyc02g077420.2.1 Solyc03g005260.2.1 
##                 33                 34                 34 
## Solyc03g044960.1.1 Solyc03g115670.1.1 Solyc04g047670.2.1 
##                 34                 34                 34 
## Solyc05g007120.2.1 Solyc06g059760.2.1 Solyc06g062550.2.1 
##                 34                 34                 34 
## Solyc06g064720.1.1 Solyc06g064920.1.1 Solyc07g008590.1.1 
##                 34                 34                 34 
## Solyc07g054750.1.1 Solyc07g061880.1.1 Solyc07g064180.2.1 
##                 34                 34                 34 
## Solyc08g060870.1.1 Solyc08g065790.2.1 Solyc08g067620.2.1 
##                 34                 34                 34 
## Solyc10g079300.1.1 Solyc11g050730.1.1 Solyc12g008650.1.1 
##                 34                 34                 34 
## Solyc01g065490.2.1 Solyc02g061900.1.1 Solyc03g026280.2.1 
##                 35                 35                 35 
## Solyc03g063220.1.1 Solyc03g116050.1.1 Solyc04g015380.1.1 
##                 35                 35                 35 
## Solyc04g076700.2.1 Solyc05g005280.2.1 Solyc08g079310.2.1 
##                 35                 35                 35 
## Solyc10g007360.2.1 Solyc10g011940.1.1 Solyc11g044340.1.1 
##                 35                 35                 35 
## Solyc11g067330.1.1 Solyc12g099430.1.1 Solyc01g005310.2.1 
##                 35                 35                 36 
## Solyc01g007980.2.1 Solyc01g102870.1.1 Solyc01g111460.2.1 
##                 36                 36                 36 
## Solyc02g085880.1.1 Solyc02g089540.2.1 Solyc03g025780.2.1 
##                 36                 36                 36 
## Solyc04g009290.1.1 Solyc07g008600.1.1 Solyc07g053730.2.1 
##                 36                 36                 36 
## Solyc08g068610.2.1 Solyc09g014530.2.1 Solyc10g026520.1.1 
##                 36                 36                 36 
## Solyc10g048100.1.1 Solyc12g042250.1.1 Solyc01g010430.2.1 
##                 36                 36                 37 
## Solyc01g010440.2.1 Solyc01g044460.1.1 Solyc01g088470.2.1 
##                 37                 37                 37 
## Solyc01g104510.2.1 Solyc01g109170.2.1 Solyc02g079440.1.1 
##                 37                 37                 37 
## Solyc02g085700.1.1 Solyc02g086410.1.1 Solyc02g088980.1.1 
##                 37                 37                 37 
## Solyc02g092680.1.1 Solyc03g065250.2.1 Solyc04g049520.1.1 
##                 37                 37                 37 
## Solyc04g071800.2.1 Solyc05g053570.2.1 Solyc07g040920.2.1 
##                 37                 37                 37 
## Solyc07g049550.2.1 Solyc08g080210.2.1 Solyc09g050050.1.1 
##                 37                 37                 37 
## Solyc09g083210.2.1 Solyc10g049210.1.1 Solyc12g010100.1.1 
##                 37                 37                 37 
## Solyc12g017610.1.1 Solyc12g049150.1.1 Solyc12g100090.1.1 
##                 37                 37                 37 
## Solyc01g097450.2.1 Solyc02g063470.1.1 Solyc03g045020.2.1 
##                 38                 38                 38 
## Solyc03g111940.2.1 Solyc04g005740.1.1 Solyc05g005980.2.1 
##                 38                 38                 38 
## Solyc06g084100.2.1 Solyc08g068130.1.1 Solyc09g056260.2.1 
##                 38                 38                 38 
## Solyc10g044490.1.1 Solyc12g011380.1.1 Solyc12g100100.1.1 
##                 38                 38                 38 
## Solyc01g057520.2.1 Solyc01g067780.1.1 Solyc01g096620.2.1 
##                 39                 39                 39 
## Solyc01g098020.2.1 Solyc01g100920.2.1 Solyc02g079460.1.1 
##                 39                 39                 39 
## Solyc03g115390.2.1 Solyc04g064770.1.1 Solyc06g043080.2.1 
##                 39                 39                 39 
## Solyc06g073750.2.1 Solyc07g008310.2.1 Solyc08g068680.2.1 
##                 39                 39                 39 
## Solyc11g044370.1.1 Solyc01g007960.2.1 Solyc01g056850.2.1 
##                 39                 40                 40 
## Solyc01g110330.1.1 Solyc02g069460.2.1 Solyc02g086430.2.1 
##                 40                 40                 40 
## Solyc04g009900.2.1 Solyc04g014320.1.1 Solyc06g073230.2.1 
##                 40                 40                 40 
## Solyc09g005870.1.1 Solyc09g064660.2.1 Solyc10g007230.1.1 
##                 40                 40                 40 
## Solyc10g085280.1.1 Solyc11g017170.1.1 Solyc11g017370.1.1 
##                 40                 40                 40 
## Solyc11g043150.1.1 Solyc11g065160.1.1 Solyc11g072980.1.1 
##                 40                 40                 40 
## Solyc12g044780.1.1 Solyc12g094730.1.1 Solyc12g099700.1.1 
##                 40                 40                 40 
## Solyc01g091100.2.1 Solyc01g111800.2.1 Solyc02g066830.2.1 
##                 41                 41                 41 
## Solyc03g013140.1.1 Solyc03g083730.1.1 Solyc03g111990.2.1 
##                 41                 41                 41 
## Solyc03g112600.2.1 Solyc05g012310.2.1 Solyc05g055710.2.1 
##                 41                 41                 41 
## Solyc06g053950.1.1 Solyc06g073540.2.1 Solyc06g074770.2.1 
##                 41                 41                 41 
## Solyc07g042790.1.1 Solyc10g009450.1.1 Solyc10g048080.1.1 
##                 41                 41                 41 
## Solyc11g030570.1.1 Solyc12g019600.1.1 Solyc01g106470.2.1 
##                 41                 41                 42 
## Solyc01g111680.2.1 Solyc03g097590.2.1 Solyc04g005650.1.1 
##                 42                 42                 42 
## Solyc04g015470.2.1 Solyc04g074000.2.1 Solyc04g074380.2.1 
##                 42                 42                 42 
## Solyc04g077180.1.1 Solyc05g008950.2.1 Solyc06g075060.1.1 
##                 42                 42                 42 
## Solyc07g049240.2.1 Solyc08g077930.2.1 Solyc09g009580.2.1 
##                 42                 42                 42 
## Solyc09g059490.1.1 Solyc11g008260.1.1 Solyc11g067030.1.1 
##                 42                 42                 42 
## Solyc01g089920.2.1 Solyc01g105730.1.1 Solyc01g110060.2.1 
##                 43                 43                 43 
## Solyc02g080840.1.1 Solyc02g082390.1.1 Solyc02g087070.2.1 
##                 43                 43                 43 
## Solyc03g019980.1.1 Solyc04g049110.1.1 Solyc04g054290.1.1 
##                 43                 43                 43 
## Solyc05g013300.1.1 Solyc07g051920.1.1 Solyc08g080900.2.1 
##                 43                 43                 43 
## Solyc12g099350.1.1 Solyc01g006610.1.1 Solyc01g058700.1.1 
##                 43                 44                 44 
## Solyc01g066100.1.1 Solyc01g091190.2.1 Solyc01g105520.2.1 
##                 44                 44                 44 
## Solyc02g031910.2.1 Solyc02g077520.2.1 Solyc03g005780.1.1 
##                 44                 44                 44 
## Solyc05g054540.2.1 Solyc06g082600.2.1 Solyc09g083370.2.1 
##                 44                 44                 44 
## Solyc12g015910.1.1 Solyc12g088160.1.1 Solyc01g099060.1.1 
##                 44                 44                 45 
## Solyc03g020060.2.1 Solyc03g078530.1.1 Solyc03g114500.2.1 
##                 45                 45                 45 
## Solyc04g063440.1.1 Solyc06g051170.2.1 Solyc06g051510.2.1 
##                 45                 45                 45 
## Solyc07g008570.2.1 Solyc08g062880.1.1 Solyc10g005390.2.1 
##                 45                 45                 45 
## Solyc11g011350.1.1 Solyc11g013870.1.1 Solyc11g071600.1.1 
##                 45                 45                 45 
## Solyc01g094260.2.1 Solyc01g102480.2.1 Solyc02g050170.1.1 
##                 46                 46                 46 
## Solyc02g069900.1.1 Solyc05g012820.1.1 Solyc09g014660.1.1 
##                 46                 46                 46 
## Solyc12g100190.1.1 Solyc01g011250.1.1 Solyc01g014910.1.1 
##                 46                 47                 47 
## Solyc01g087290.2.1 Solyc01g109400.2.1 Solyc01g111450.2.1 
##                 47                 47                 47 
## Solyc02g072010.1.1 Solyc03g060500.1.1 Solyc04g074630.2.1 
##                 47                 47                 47 
## Solyc06g074160.1.1 Solyc09g010000.2.1 Solyc10g074600.1.1 
##                 47                 47                 47 
## Solyc11g013730.1.1 Solyc12g036870.1.1 Solyc01g103070.2.1 
##                 47                 47                 48 
## Solyc02g083640.2.1 Solyc05g047640.2.1 Solyc06g030570.2.1 
##                 48                 48                 48 
## Solyc08g006750.2.1 Solyc10g080280.1.1 Solyc11g017040.1.1 
##                 48                 48                 48 
## Solyc12g019110.1.1 Solyc12g098870.1.1 Solyc02g032220.1.1 
##                 48                 48                 49 
## Solyc02g071060.2.1 Solyc02g083020.1.1 Solyc02g087150.2.1 
##                 49                 49                 49 
## Solyc03g005950.1.1 Solyc03g063470.1.1 Solyc04g017610.2.1 
##                 49                 49                 49 
## Solyc04g048980.2.1 Solyc05g050430.1.1 Solyc06g069160.1.1 
##                 49                 49                 49 
## Solyc06g071980.2.1 Solyc07g051930.1.1 Solyc07g052220.1.1 
##                 49                 49                 49 
## Solyc08g042030.1.1 Solyc08g079970.1.1 Solyc11g020850.1.1 
##                 49                 49                 49 
## Solyc12g088090.1.1 Solyc01g098980.2.1 Solyc02g032040.1.1 
##                 49                 50                 50 
## Solyc03g063980.1.1 Solyc05g009040.2.1 Solyc05g055580.1.1 
##                 50                 50                 50 
## Solyc06g036750.1.1 Solyc07g054120.1.1 Solyc08g048210.1.1 
##                 50                 50                 50 
## Solyc08g062980.1.1 Solyc11g012670.1.1 Solyc01g088030.2.1 
##                 50                 50                 51 
## Solyc02g079550.1.1 Solyc02g080300.2.1 Solyc03g034030.2.1 
##                 51                 51                 51 
## Solyc03g120560.2.1 Solyc04g074560.1.1 Solyc05g015930.2.1 
##                 51                 51                 51 
## Solyc07g043660.2.1 Solyc07g061730.2.1 Solyc11g010760.1.1 
##                 51                 51                 51 
## Solyc12g007210.1.1 Solyc12g049170.1.1 Solyc02g091350.2.1 
##                 51                 51                 52 
## Solyc03g115280.1.1 Solyc03g123950.2.1 Solyc04g047780.1.1 
##                 52                 52                 52 
## Solyc04g072830.2.1 Solyc06g051780.2.1 Solyc06g053220.2.1 
##                 52                 52                 52 
## Solyc07g014640.2.1 Solyc08g022240.1.1 Solyc09g059170.1.1 
##                 52                 52                 52 
## Solyc11g013890.1.1 Solyc12g038830.1.1 Solyc01g066040.2.1 
##                 52                 52                 53 
## Solyc01g106140.1.1 Solyc03g034460.2.1 Solyc03g063480.2.1 
##                 53                 53                 53 
## Solyc03g120670.2.1 Solyc04g010200.1.1 Solyc04g015210.2.1 
##                 53                 53                 53 
## Solyc05g018200.1.1 Solyc06g009290.2.1 Solyc06g073480.2.1 
##                 53                 53                 53 
## Solyc07g054540.2.1 Solyc08g074590.2.1 Solyc08g076200.2.1 
##                 53                 53                 53 
## Solyc09g082240.2.1 Solyc10g084950.1.1 Solyc11g045250.1.1 
##                 53                 53                 53 
## Solyc11g071540.1.1 Solyc01g079340.2.1 Solyc01g098300.1.1 
##                 53                 54                 54 
## Solyc02g072040.2.1 Solyc03g006780.2.1 Solyc04g064720.2.1 
##                 54                 54                 54 
## Solyc09g074280.1.1 Solyc10g079400.1.1 Solyc12g049160.1.1 
##                 54                 54                 54 
## Solyc01g056210.1.1 Solyc03g093410.2.1 Solyc05g041830.2.1 
##                 55                 55                 55 
## Solyc05g044510.1.1 Solyc06g083000.1.1 Solyc08g067560.1.1 
##                 55                 55                 55 
## Solyc09g074980.2.1 Solyc11g006530.1.1 Solyc11g072420.1.1 
##                 55                 55                 55 
## Solyc12g014530.1.1 Solyc01g091130.2.1 Solyc01g110000.2.1 
##                 55                 56                 56 
## Solyc01g111230.2.1 Solyc02g071380.2.1 Solyc02g080240.1.1 
##                 56                 56                 56 
## Solyc02g081370.2.1 Solyc03g112110.1.1 Solyc04g057790.1.1 
##                 56                 56                 56 
## Solyc05g018280.1.1 Solyc05g052570.2.1 Solyc06g063190.2.1 
##                 56                 56                 56 
## Solyc08g015840.1.1 Solyc08g075210.1.1 Solyc10g078820.1.1 
##                 56                 56                 56 
## Solyc10g083890.1.1 Solyc01g107970.1.1 Solyc02g072460.1.1 
##                 56                 57                 57 
## Solyc06g059720.2.1 Solyc07g040790.2.1 Solyc08g006050.1.1 
##                 57                 57                 57 
## Solyc10g007430.1.1 Solyc01g081270.2.1 Solyc02g061690.1.1 
##                 57                 58                 58 
## Solyc04g024880.1.1 Solyc04g052970.1.1 Solyc05g005420.1.1 
##                 58                 58                 58 
## Solyc05g050910.2.1 Solyc06g053570.2.1 Solyc07g006470.1.1 
##                 58                 58                 58 
## Solyc07g007840.1.1 Solyc07g032180.2.1 Solyc07g052190.1.1 
##                 58                 58                 58 
## Solyc08g048140.1.1 Solyc09g007890.1.1 Solyc12g049540.1.1 
##                 58                 58                 58 
## Solyc12g056110.1.1 Solyc03g033760.1.1 Solyc03g083440.2.1 
##                 58                 59                 59 
## Solyc08g082230.2.1 Solyc11g013280.1.1 Solyc01g094440.1.1 
##                 59                 59                 60 
## Solyc01g095260.1.1 Solyc02g092670.1.1 Solyc03g058380.2.1 
##                 60                 60                 60 
## Solyc03g111460.1.1 Solyc03g117370.2.1 Solyc04g079810.1.1 
##                 60                 60                 60 
## Solyc04g080870.1.1 Solyc05g006290.1.1 Solyc06g065980.2.1 
##                 60                 60                 60 
## Solyc07g053230.2.1 Solyc09g007920.2.1 Solyc10g055580.1.1 
##                 60                 60                 60 
## Solyc11g020260.1.1 Solyc11g040240.1.1 Solyc01g087450.2.1 
##                 60                 60                 61 
## Solyc02g011680.2.1 Solyc02g063480.2.1 Solyc04g024500.2.1 
##                 61                 61                 61 
## Solyc05g012020.2.1 Solyc05g013890.1.1 Solyc05g050360.2.1 
##                 61                 61                 61 
## Solyc06g064470.2.1 Solyc08g065690.1.1 Solyc10g024400.1.1 
##                 61                 61                 61 
## Solyc11g007730.1.1 Solyc11g045190.1.1 Solyc02g085080.2.1 
##                 61                 61                 62 
## Solyc02g091730.1.1 Solyc05g052680.1.1 Solyc07g006620.2.1 
##                 62                 62                 62 
## Solyc07g007770.1.1 Solyc11g044620.1.1 Solyc01g104720.2.1 
##                 62                 62                 63 
## Solyc01g109200.2.1 Solyc02g083680.1.1 Solyc03g083790.1.1 
##                 63                 63                 63 
## Solyc08g074300.2.1 Solyc08g075480.2.1 Solyc01g059760.1.1 
##                 63                 63                 64 
## Solyc08g061240.1.1 Solyc09g005900.2.1 Solyc10g018110.1.1 
##                 64                 64                 64 
## Solyc10g049370.1.1 Solyc10g079520.1.1 Solyc11g012300.1.1 
##                 64                 64                 64 
## Solyc06g062560.1.1 Solyc09g092380.2.1 Solyc10g076500.1.1 
##                 65                 65                 65 
## Solyc01g079550.2.1 Solyc01g111010.2.1 Solyc03g111500.2.1 
##                 66                 66                 66 
## Solyc07g052540.2.1 Solyc10g084200.1.1 Solyc11g007290.1.1 
##                 66                 66                 66 
## Solyc11g011310.1.1 Solyc12g097010.1.1 Solyc01g010340.1.1 
##                 66                 66                 67 
## Solyc01g098690.2.1 Solyc01g104100.2.1 Solyc01g111260.2.1 
##                 67                 67                 67 
## Solyc07g021330.1.1 Solyc07g064380.2.1 Solyc09g013100.2.1 
##                 67                 67                 67 
## Solyc01g073980.1.1 Solyc01g110900.1.1 Solyc02g062320.2.1 
##                 68                 68                 68 
## Solyc03g093550.1.1 Solyc03g111770.2.1 Solyc03g118110.2.1 
##                 68                 68                 68 
## Solyc04g051790.1.1 Solyc06g072940.1.1 Solyc08g036500.1.1 
##                 68                 68                 68 
## Solyc01g108810.2.1 Solyc02g014740.1.1 Solyc02g082410.2.1 
##                 69                 69                 69 
## Solyc05g009750.1.1 Solyc06g005920.1.1 Solyc06g082560.1.1 
##                 69                 69                 69 
## Solyc07g016020.1.1 Solyc10g083830.1.1 Solyc11g056410.1.1 
##                 69                 69                 69 
## Solyc12g008340.1.1 Solyc12g038430.1.1 Solyc12g096740.1.1 
##                 69                 69                 69 
## Solyc01g110930.1.1 Solyc02g081480.2.1 Solyc07g042950.1.1 
##                 70                 70                 70 
## Solyc11g010230.1.1 Solyc11g028070.1.1 Solyc01g110030.2.1 
##                 70                 70                 71 
## Solyc04g074390.2.1 Solyc05g023700.1.1 Solyc05g050960.2.1 
##                 71                 71                 71 
## Solyc06g053870.2.1 Solyc01g096980.1.1 Solyc03g006350.2.1 
##                 71                 72                 72 
## Solyc07g006930.1.1 Solyc09g065690.2.1 Solyc12g057080.1.1 
##                 72                 72                 72 
## Solyc01g094740.1.1 Solyc01g111480.1.1 Solyc02g043860.2.1 
##                 73                 73                 73 
## Solyc03g083170.2.1 Solyc07g006250.2.1 Solyc10g047840.1.1 
##                 73                 73                 73 
## Solyc11g032040.1.1 Solyc12g021200.1.1 Solyc01g016850.1.1 
##                 73                 73                 74 
## Solyc01g101180.2.1 Solyc01g111120.2.1 Solyc02g065350.2.1 
##                 74                 74                 74 
## Solyc02g070110.1.1 Solyc04g081130.1.1 Solyc09g083100.1.1 
##                 74                 74                 74 
## Solyc11g013830.1.1 Solyc12g040520.1.1 Solyc01g066290.2.1 
##                 74                 74                 75 
## Solyc01g079060.2.1 Solyc02g068600.2.1 Solyc06g005890.2.1 
##                 75                 75                 75 
## Solyc06g011550.2.1 Solyc06g063200.1.1 Solyc07g054900.2.1 
##                 75                 75                 75 
## Solyc08g061850.2.1 Solyc10g050530.1.1 Solyc10g078230.1.1 
##                 75                 75                 75 
## Solyc03g098310.1.1 Solyc04g077030.2.1 Solyc09g008480.2.1 
##                 76                 76                 76 
## Solyc09g089970.1.1 Solyc10g086320.1.1 Solyc02g032960.2.1 
##                 76                 76                 77 
## Solyc03g112040.1.1 Solyc04g049900.1.1 Solyc04g082010.1.1 
##                 77                 77                 77 
## Solyc05g025740.2.1 Solyc06g065360.2.1 Solyc07g025210.1.1 
##                 77                 77                 77 
## Solyc08g074620.1.1 Solyc10g037940.1.1 Solyc12g008550.1.1 
##                 77                 77                 77 
## Solyc01g009260.1.1 Solyc01g111070.2.1 Solyc02g078060.1.1 
##                 78                 78                 78 
## Solyc02g082000.2.1 Solyc03g098400.1.1 Solyc03g112030.1.1 
##                 78                 78                 78 
## Solyc07g043390.2.1 Solyc07g049190.2.1 Solyc11g011850.1.1 
##                 78                 78                 78 
## Solyc01g099520.2.1 Solyc02g067100.2.1 Solyc02g070320.2.1 
##                 79                 79                 79 
## Solyc02g080070.2.1 Solyc05g053600.2.1 Solyc06g069670.2.1 
##                 79                 79                 79 
## Solyc07g061710.1.1 Solyc09g007910.2.1 Solyc02g062810.2.1 
##                 79                 79                 80 
## Solyc02g070060.1.1 Solyc03g095240.2.1 Solyc04g080320.1.1 
##                 80                 80                 80 
## Solyc07g008550.2.1 Solyc07g008630.1.1 Solyc08g005820.1.1 
##                 80                 80                 80 
## Solyc08g021910.1.1 Solyc09g030430.1.1 Solyc10g049800.1.1 
##                 80                 80                 80 
## Solyc12g088050.1.1 Solyc04g079640.2.1 Solyc07g008920.2.1 
##                 80                 81                 81 
## Solyc01g056620.2.1 Solyc01g060080.2.1 Solyc01g088300.2.1 
##                 82                 82                 82 
## Solyc02g032450.2.1 Solyc02g086280.2.1 Solyc03g120550.2.1 
##                 82                 82                 82 
## Solyc06g064730.1.1 Solyc08g068770.1.1 Solyc09g092640.2.1 
##                 82                 82                 82 
## Solyc10g054790.1.1 Solyc11g067140.1.1 Solyc02g030110.2.1 
##                 82                 82                 83 
## Solyc02g084790.2.1 Solyc05g018620.2.1 Solyc06g071150.2.1 
##                 83                 83                 83 
## Solyc07g006050.1.1 Solyc10g018960.1.1 Solyc01g090080.1.1 
##                 83                 83                 84 
## Solyc03g078770.2.1 Solyc06g075940.1.1 Solyc06g083800.2.1 
##                 84                 84                 84 
## Solyc07g054610.2.1 Solyc02g080750.1.1 Solyc02g094540.2.1 
##                 84                 85                 85 
## Solyc04g079660.2.1 Solyc05g010640.2.1 Solyc06g054120.1.1 
##                 85                 85                 85 
## Solyc08g036480.1.1 Solyc11g010990.1.1 Solyc01g107680.2.1 
##                 85                 85                 86 
## Solyc03g097570.2.1 Solyc03g124010.2.1 Solyc02g064870.1.1 
##                 86                 86                 87 
## Solyc08g013970.1.1 Solyc08g080700.1.1 Solyc01g101190.2.1 
##                 87                 87                 88 
## Solyc10g044550.1.1 Solyc12g033060.1.1 Solyc08g014110.1.1 
##                 88                 88                 90 
## Solyc10g084590.2.1 Solyc12g049240.1.1 Solyc02g062860.2.1 
##                 90                 90                 91 
## Solyc05g013870.2.1 Solyc08g062250.1.1 Solyc08g062650.2.1 
##                 91                 91                 91 
## Solyc02g062290.2.1 Solyc02g094610.1.1 Solyc04g078440.2.1 
##                 92                 92                 92 
## Solyc06g054670.1.1 Solyc09g092310.1.1 Solyc12g088520.1.1 
##                 92                 92                 92 
## Solyc02g084640.2.1 Solyc02g086110.2.1 Solyc03g026330.2.1 
##                 93                 93                 93 
## Solyc05g005590.2.1 Solyc05g009760.1.1 Solyc08g075600.1.1 
##                 93                 93                 93 
## Solyc12g021340.1.1 Solyc01g097390.2.1 Solyc07g042630.2.1 
##                 93                 94                 94 
## Solyc09g009370.2.1 Solyc01g111210.2.1 Solyc04g054800.2.1 
##                 94                 95                 95 
## Solyc07g020930.1.1 Solyc11g013480.1.1 Solyc03g113880.2.1 
##                 95                 95                 96 
## Solyc04g051610.2.1 Solyc05g055590.1.1 Solyc12g096770.1.1 
##                 96                 96                 96 
## Solyc04g055140.1.1 Solyc08g013800.2.1 Solyc09g005030.1.1 
##                 97                 97                 97 
## Solyc09g008720.1.1 Solyc11g008530.1.1 Solyc01g015050.1.1 
##                 97                 97                 98 
## Solyc06g076640.2.1 Solyc10g076590.1.1 Solyc11g072320.1.1 
##                 98                 98                 98 
## Solyc01g098370.1.1 Solyc02g068940.1.1 Solyc04g049380.2.1 
##                 99                 99                 99 
## Solyc10g045410.1.1 Solyc12g070170.1.1 Solyc01g103720.2.1 
##                 99                 99                100 
## Solyc01g108280.2.1 Solyc02g080220.2.1 Solyc08g077500.2.1 
##                100                100                100 
## Solyc09g066370.1.1 Solyc10g008180.1.1 Solyc07g051890.1.1 
##                100                100                101 
## Solyc09g082840.1.1 Solyc09g091180.2.1 Solyc12g100080.1.1 
##                101                101                101 
## Solyc02g063360.2.1 Solyc07g008080.2.1 Solyc09g018430.2.1 
##                102                102                102 
## Solyc03g093760.1.1 Solyc03g095680.1.1 Solyc04g010130.1.1 
##                103                103                103 
## Solyc07g022790.2.1 Solyc11g010740.1.1 Solyc03g025600.2.1 
##                103                103                104 
## Solyc03g061600.2.1 Solyc03g078810.2.1 Solyc04g024990.1.1 
##                104                104                104 
## Solyc04g076310.2.1 Solyc04g077090.1.1 Solyc10g079600.1.1 
##                104                104                104 
## Solyc01g104480.2.1 Solyc04g058030.1.1 Solyc03g098540.1.1 
##                105                105                106 
## Solyc07g055380.1.1 Solyc07g056470.2.1 Solyc10g074440.1.1 
##                106                106                106 
## Solyc11g072860.1.1 Solyc03g006450.1.1 Solyc03g111210.2.1 
##                106                107                107 
## Solyc04g051410.2.1 Solyc10g006260.2.1 Solyc12g005100.1.1 
##                107                107                107 
## Solyc10g018630.1.1 Solyc02g084360.2.1 Solyc03g111930.2.1 
##                108                109                109 
## Solyc05g008760.2.1 Solyc11g042900.1.1 Solyc01g088060.2.1 
##                109                109                110 
## Solyc01g111080.2.1 Solyc11g006630.1.1 Solyc01g006350.2.1 
##                110                110                111 
## Solyc03g007950.2.1 Solyc07g018110.1.1 Solyc01g111000.2.1 
##                111                111                112 
## Solyc02g081740.1.1 Solyc07g009430.1.1 Solyc09g005590.2.1 
##                112                112                112 
## Solyc11g005830.1.1 Solyc12g005480.1.1 Solyc01g011480.1.1 
##                112                112                113 
## Solyc03g053080.1.1 Solyc06g075420.1.1 Solyc10g055810.1.1 
##                113                113                113 
## Solyc12g035850.1.1 Solyc12g096170.1.1 Solyc01g108700.2.1 
##                113                113                114 
## Solyc04g072330.1.1 Solyc06g082240.2.1 Solyc07g043630.1.1 
##                114                114                114 
## Solyc09g092710.2.1 Solyc12g043070.1.1 Solyc01g087010.2.1 
##                114                114                115 
## Solyc01g094210.2.1 Solyc03g122170.2.1 Solyc05g005900.2.1 
##                115                115                115 
## Solyc11g020770.1.1 Solyc01g087300.2.1 Solyc01g100160.2.1 
##                115                116                116 
## Solyc12g077430.1.1 Solyc09g072640.2.1 Solyc03g082770.1.1 
##                116                117                118 
## Solyc03g096700.1.1 Solyc01g106920.2.1 Solyc02g032140.1.1 
##                118                119                119 
## Solyc08g044300.1.1 Solyc08g065750.1.1 Solyc10g051140.1.1 
##                119                119                119 
## Solyc12g038530.1.1 Solyc05g014540.2.1 Solyc10g055270.1.1 
##                119                120                120 
## Solyc11g012340.1.1 Solyc12g042630.1.1 Solyc12g039010.1.1 
##                120                121                122 
## Solyc01g059910.2.1 Solyc02g077170.1.1 Solyc02g084180.1.1 
##                123                123                123 
## Solyc06g075440.1.1 Solyc11g020660.1.1 Solyc04g009860.2.1 
##                123                123                124 
## Solyc04g072480.2.1 Solyc09g005480.2.1 Solyc09g011960.1.1 
##                124                124                124 
## Solyc11g020020.1.1 Solyc11g071480.1.1 Solyc01g010460.2.1 
##                124                124                125 
## Solyc01g103910.1.1 Solyc01g109040.2.1 Solyc04g008120.1.1 
##                125                125                125 
## Solyc09g018690.2.1 Solyc05g052670.1.1 Solyc06g008090.2.1 
##                125                126                126 
## Solyc04g058110.2.1 Solyc06g064750.1.1 Solyc08g065500.1.1 
##                127                127                127 
## Solyc09g089760.1.1 Solyc12g070270.1.1 Solyc01g017490.1.1 
##                128                128                129 
## Solyc02g071100.2.1 Solyc08g007390.2.1 Solyc01g103200.2.1 
##                129                129                130 
## Solyc12g089370.1.1 Solyc07g009580.1.1 Solyc08g008670.2.1 
##                130                131                131 
## Solyc08g066010.2.1 Solyc01g068610.2.1 Solyc01g106620.2.1 
##                131                132                132 
## Solyc02g088780.2.1 Solyc04g055240.1.1 Solyc08g068120.1.1 
##                132                132                132 
## Solyc02g089840.2.1 Solyc06g065870.2.1 Solyc02g021700.2.1 
##                134                135                136 
## Solyc02g088870.1.1 Solyc05g014090.1.1 Solyc08g068690.1.1 
##                136                136                136 
## Solyc11g042470.1.1 Solyc01g103740.2.1 Solyc11g066550.1.1 
##                136                137                137 
## Solyc01g007000.2.1 Solyc05g011940.2.1 Solyc05g026330.1.1 
##                138                138                138 
## Solyc10g052690.1.1 Solyc11g018520.1.1 Solyc01g102580.2.1 
##                138                138                139 
## Solyc03g111280.1.1 Solyc08g076770.2.1 Solyc10g049400.1.1 
##                139                139                139 
## Solyc04g076710.2.1 Solyc08g074460.1.1 Solyc12g008900.1.1 
##                140                140                140 
## Solyc11g033250.1.1 Solyc01g017930.1.1 Solyc04g017890.1.1 
##                141                142                142 
## Solyc05g008750.2.1 Solyc07g062500.2.1 Solyc02g080390.2.1 
##                143                143                144 
## Solyc05g018330.1.1 Solyc07g045410.1.1 Solyc09g055970.1.1 
##                144                144                144 
## Solyc01g111200.2.1 Solyc07g051880.1.1 Solyc10g085340.1.1 
##                145                145                145 
## Solyc12g038130.1.1 Solyc01g010720.2.1 Solyc03g007850.1.1 
##                145                146                146 
## Solyc05g041580.1.1 Solyc02g032720.1.1 Solyc02g081770.1.1 
##                146                147                147 
## Solyc08g067210.2.1 Solyc03g118710.2.1 Solyc09g055390.1.1 
##                147                148                148 
## Solyc05g005360.1.1 Solyc11g063610.1.1 Solyc04g052960.1.1 
##                149                149                150 
## Solyc10g079670.1.1 Solyc01g007890.1.1 Solyc09g082690.2.1 
##                150                151                151 
## Solyc01g097700.1.1 Solyc04g009110.1.1 Solyc02g086990.2.1 
##                152                152                153 
## Solyc03g122350.2.1 Solyc11g011620.1.1 Solyc08g066320.2.1 
##                153                153                154 
## Solyc11g056330.1.1 Solyc02g076750.1.1 Solyc06g071870.2.1 
##                155                156                156 
## Solyc03g094080.2.1 Solyc04g049760.2.1 Solyc01g110800.2.1 
##                157                157                158 
## Solyc03g051930.2.1 Solyc06g068190.1.1 Solyc01g006410.2.1 
##                158                158                159 
## Solyc02g081360.2.1 Solyc02g085950.2.1 Solyc02g089850.2.1 
##                159                160                160 
## Solyc05g054340.2.1 Solyc03g093280.1.1 Solyc11g007030.1.1 
##                160                161                161 
## Solyc11g045160.1.1 Solyc02g088270.2.1 Solyc03g053010.2.1 
##                161                162                162 
## Solyc07g055440.1.1 Solyc02g071030.1.1 Solyc07g062230.2.1 
##                162                163                163 
## Solyc01g110890.1.1 Solyc03g025250.2.1 Solyc09g074130.1.1 
##                164                164                164 
## Solyc12g010950.1.1 Solyc08g079010.1.1 Solyc11g005520.1.1 
##                164                165                165 
## Solyc02g084520.2.1 Solyc04g005850.1.1 Solyc07g026960.2.1 
##                166                166                166 
## Solyc07g063730.1.1 Solyc03g083130.1.1 Solyc01g105740.1.1 
##                166                167                168 
## Solyc02g038650.1.1 Solyc02g062480.1.1 Solyc09g005090.1.1 
##                168                168                168 
## Solyc09g015020.1.1 Solyc01g008360.2.1 Solyc05g007540.1.1 
##                168                169                169 
## Solyc01g008290.2.1 Solyc11g069310.1.1 Solyc05g007630.2.1 
##                170                170                171 
## Solyc01g099730.2.1 Solyc08g065570.1.1 Solyc08g067870.1.1 
##                172                172                172 
## Solyc12g098840.1.1 Solyc06g070920.2.1 Solyc07g017710.1.1 
##                172                173                174 
## Solyc10g009540.1.1 Solyc10g080380.1.1 Solyc01g068340.2.1 
##                174                174                175 
## Solyc01g090260.2.1 Solyc01g091300.2.1 Solyc01g102540.2.1 
##                175                175                175 
## Solyc01g108820.1.1 Solyc06g073530.1.1 Solyc12g088620.1.1 
##                175                175                175 
## Solyc04g050380.1.1 Solyc06g075490.1.1 Solyc08g065250.2.1 
##                176                176                176 
## Solyc10g007460.2.1 Solyc01g049820.2.1 Solyc01g091050.2.1 
##                178                180                180 
## Solyc11g008540.1.1 Solyc11g012810.1.1 Solyc03g070400.1.1 
##                180                180                181 
## Solyc01g107300.2.1 Solyc01g005880.1.1 Solyc03g118930.2.1 
##                183                184                184 
## Solyc10g083280.1.1 Solyc08g068780.1.1 Solyc09g098470.1.1 
##                184                185                185 
## Solyc10g078490.1.1 Solyc12g076350.1.1 Solyc07g017700.1.1 
##                185                185                186 
## Solyc08g006740.2.1 Solyc09g066030.1.1 Solyc06g068060.2.1 
##                186                186                188 
## Solyc10g076970.1.1 Solyc01g100680.1.1 Solyc05g015220.2.1 
##                188                189                189 
## Solyc08g063010.2.1 Solyc08g066570.1.1 Solyc01g080100.2.1 
##                189                189                190 
## Solyc08g083120.2.1 Solyc03g044790.2.1 Solyc10g085240.1.1 
##                190                191                191 
## Solyc12g089310.1.1 Solyc01g111130.2.1 Solyc04g076140.2.1 
##                191                192                192 
## Solyc01g087840.2.1 Solyc02g036340.2.1 Solyc04g014590.1.1 
##                193                194                194 
## Solyc05g010440.1.1 Solyc05g015920.2.1 Solyc01g044480.2.1 
##                194                194                195 
## Solyc04g024420.2.1 Solyc05g012890.1.1 Solyc12g089300.1.1 
##                195                195                196 
## Solyc02g066890.1.1 Solyc09g009870.2.1 Solyc12g096450.1.1 
##                197                197                197 
## Solyc03g063410.1.1 Solyc08g078710.1.1 Solyc01g090330.1.1 
##                198                198                199 
## Solyc03g031730.2.1 Solyc09g005540.1.1 Solyc03g019920.1.1 
##                199                199                201 
## Solyc01g011200.2.1 Solyc01g109160.2.1 Solyc03g114540.1.1 
##                202                202                202 
## Solyc01g080740.1.1 Solyc03g034130.2.1 Solyc03g122050.1.1 
##                203                203                203 
## Solyc05g052530.1.1 Solyc12g009780.1.1 Solyc02g077210.1.1 
##                204                204                205 
## Solyc01g106770.2.1 Solyc03g006730.1.1 Solyc04g078720.1.1 
##                207                207                207 
## Solyc06g059710.2.1 Solyc02g092030.1.1 Solyc05g046140.2.1 
##                207                208                209 
## Solyc05g010780.1.1 Solyc01g057040.2.1 Solyc01g110860.1.1 
##                211                212                213 
## Solyc06g064960.2.1 Solyc12g019020.1.1 Solyc01g106120.2.1 
##                213                213                214 
## Solyc04g010210.1.1 Solyc04g076540.2.1 Solyc04g079030.2.1 
##                214                215                215 
## Solyc01g108460.1.1 Solyc04g028470.1.1 Solyc06g054340.1.1 
##                216                216                217 
## Solyc08g065650.1.1 Solyc01g112370.2.1 Solyc01g106910.2.1 
##                218                220                221 
## Solyc03g033360.1.1 Solyc12g062720.1.1 Solyc05g043350.2.1 
##                221                221                222 
## Solyc06g068430.2.1 Solyc06g074100.1.1 Solyc06g076210.1.1 
##                222                223                223 
## Solyc06g051390.2.1 Solyc12g009690.1.1 Solyc02g030130.2.1 
##                224                226                227 
## Solyc01g095320.2.1 Solyc03g115300.1.1 Solyc11g005040.1.1 
##                228                228                229 
## Solyc02g081100.1.1 Solyc02g092350.2.1 Solyc01g006040.2.1 
##                230                231                234 
## Solyc07g018100.2.1 Solyc01g016540.1.1 Solyc03g119240.2.1 
##                234                235                236 
## Solyc03g031430.1.1 Solyc06g065150.1.1 Solyc02g086070.2.1 
##                237                237                238 
## Solyc05g007250.2.1 Solyc01g007250.2.1 Solyc07g008500.1.1 
##                238                239                239 
## Solyc11g006640.1.1 Solyc10g074610.1.1 Solyc07g056610.1.1 
##                239                240                241 
## Solyc08g075630.2.1 Solyc01g110940.2.1 Solyc05g014380.2.1 
##                241                242                243 
## Solyc04g076440.1.1 Solyc01g106810.2.1 Solyc02g085860.2.1 
##                244                245                247 
## Solyc01g111150.2.1 Solyc03g043650.1.1 Solyc01g110080.1.1 
##                248                248                249 
## Solyc09g075940.2.1 Solyc10g006610.2.1 Solyc11g011070.1.1 
##                249                249                249 
## Solyc09g064470.2.1 Solyc06g074870.1.1 Solyc08g061810.2.1 
##                251                252                252 
## Solyc04g050150.2.1 Solyc05g043210.1.1 Solyc03g114260.1.1 
##                253                253                254 
## Solyc12g049090.1.1 Solyc02g014550.1.1 Solyc03g026130.2.1 
##                254                255                255 
## Solyc01g008540.2.1 Solyc07g041510.1.1 Solyc09g075930.1.1 
##                256                256                256 
## Solyc11g013070.1.1 Solyc02g011690.1.1 Solyc03g111290.1.1 
##                256                258                258 
## Solyc09g092020.2.1 Solyc01g097000.2.1 Solyc01g111170.2.1 
##                258                260                260 
## Solyc03g063280.2.1 Solyc08g077610.1.1 Solyc10g044980.1.1 
##                260                260                260 
## Solyc04g005190.2.1 Solyc05g055110.2.1 Solyc12g035500.1.1 
##                261                261                261 
## Solyc06g007300.1.1 Solyc11g007990.1.1 Solyc07g021460.1.1 
##                263                263                264 
## Solyc06g066520.1.1 Solyc07g042800.2.1 Solyc02g094700.1.1 
##                267                267                269 
## Solyc05g026480.1.1 Solyc06g074450.1.1 Solyc09g009320.1.1 
##                270                270                271 
## Solyc09g064390.2.1 Solyc12g055780.1.1 Solyc01g034210.1.1 
##                271                273                275 
## Solyc01g112300.2.1 Solyc11g069620.1.1 Solyc06g050610.1.1 
##                277                277                278 
## Solyc09g064310.2.1 Solyc05g054020.1.1 Solyc10g007240.1.1 
##                278                279                279 
## Solyc01g081080.1.1 Solyc02g031860.2.1 Solyc03g122290.2.1 
##                284                285                285 
## Solyc05g026520.1.1 Solyc06g048710.1.1 Solyc01g009690.1.1 
##                287                288                289 
## Solyc02g092020.1.1 Solyc10g074430.1.1 Solyc09g090610.2.1 
##                289                289                290 
## Solyc01g099740.2.1 Solyc08g080450.1.1 Solyc01g112310.2.1 
##                292                292                293 
## Solyc01g110880.1.1 Solyc05g009000.2.1 Solyc06g084240.1.1 
##                294                294                295 
## Solyc01g009830.2.1 Solyc01g111020.2.1 Solyc01g111040.2.1 
##                296                296                297 
## Solyc04g005700.2.1 Solyc11g008470.1.1 Solyc08g068010.1.1 
##                299                303                304 
## Solyc11g050710.1.1 Solyc01g091040.2.1 Solyc01g110920.2.1 
##                305                306                306 
## Solyc04g039990.2.1 Solyc06g042950.2.1 Solyc11g071620.1.1 
##                306                307                310 
## Solyc09g083250.2.1 Solyc12g049070.1.1 Solyc12g009870.1.1 
##                311                311                312 
## Solyc12g056730.1.1 Solyc09g015830.1.1 Solyc05g052810.2.1 
##                315                316                318 
## Solyc06g010200.2.1 Solyc02g079610.2.1 Solyc02g092310.2.1 
##                323                326                326 
## Solyc05g006170.2.1 Solyc09g065080.1.1 Solyc05g014020.1.1 
##                326                328                329 
## Solyc11g065470.1.1 Solyc01g008860.1.1 Solyc02g089340.2.1 
##                330                331                331 
## Solyc07g037940.1.1 Solyc08g061500.1.1 Solyc05g014100.1.1 
##                336                337                338 
## Solyc10g081070.1.1 Solyc06g064630.2.1 Solyc12g049430.1.1 
##                338                339                339 
## Solyc02g084500.2.1 Solyc01g112350.2.1 Solyc11g071430.1.1 
##                340                341                341 
## Solyc01g067220.1.1 Solyc03g111810.2.1 Solyc12g098780.1.1 
##                342                342                342 
## Solyc06g064980.2.1 Solyc01g091110.2.1 Solyc05g012360.2.1 
##                345                346                346 
## Solyc07g051870.1.1 Solyc01g091020.2.1 Solyc08g083450.1.1 
##                350                351                351 
## Solyc10g083750.1.1 Solyc12g019270.1.1 Solyc08g065590.1.1 
##                353                356                358 
## Solyc01g106800.2.1 Solyc04g076910.2.1 Solyc01g087790.2.1 
##                359                361                363 
## Solyc03g111570.2.1 Solyc11g005840.1.1 Solyc01g095940.2.1 
##                363                363                365 
## Solyc03g119880.2.1 Solyc07g009510.1.1 Solyc12g056710.1.1 
##                367                370                370 
## Solyc03g020000.2.1 Solyc12g010610.1.1 Solyc06g061210.2.1 
##                371                374                377 
## Solyc01g111110.2.1 Solyc04g076450.1.1 Solyc04g071270.1.1 
##                380                381                382 
## Solyc07g065430.2.1 Solyc02g089050.2.1 Solyc09g005450.1.1 
##                382                385                386 
## Solyc10g085390.1.1 Solyc11g066990.1.1 Solyc01g086940.2.1 
##                387                388                390 
## Solyc07g066010.2.1 Solyc01g110020.2.1 Solyc05g056070.2.1 
##                395                403                403 
## Solyc08g006200.1.1 Solyc08g015710.1.1 Solyc01g065910.1.1 
##                408                408                409 
## Solyc02g071240.2.1 Solyc04g056410.2.1 Solyc07g032320.1.1 
##                412                412                414 
## Solyc05g055550.2.1 Solyc07g064170.2.1 Solyc10g051100.1.1 
##                416                416                418 
## Solyc07g041330.1.1 Solyc01g056280.2.1 Solyc08g006260.1.1 
##                419                421                424 
## Solyc12g027580.1.1 Solyc07g062760.1.1 Solyc11g022400.1.1 
##                426                429                433 
## Solyc06g075870.1.1 Solyc02g080010.2.1 Solyc12g005900.1.1 
##                434                437                440 
## Solyc07g063710.1.1 Solyc11g012220.1.1 Solyc07g005480.2.1 
##                445                446                452 
## Solyc02g050260.2.1 Solyc05g016440.2.1 Solyc02g068820.1.1 
##                453                456                457 
## Solyc03g117920.1.1 Solyc06g071620.2.1 Solyc10g007160.1.1 
##                459                460                460 
## Solyc04g076990.2.1 Solyc05g005550.2.1 Solyc05g055820.2.1 
##                466                467                470 
## Solyc09g057920.2.1 Solyc02g067780.2.1 Solyc06g006040.1.1 
##                470                471                471 
## Solyc01g091810.1.1 Solyc05g005960.2.1 Solyc04g082420.2.1 
##                472                472                473 
## Solyc07g051960.1.1 Solyc11g013320.1.1 Solyc03g116440.1.1 
##                473                473                474 
## Solyc12g094410.1.1 Solyc02g079850.2.1 Solyc02g077530.1.1 
##                474                477                480 
## Solyc02g055460.1.1 Solyc07g054920.1.1 Solyc02g080120.1.1 
##                482                482                485 
## Solyc03g093250.1.1 Solyc12g027800.1.1 Solyc04g015720.1.1 
##                485                486                491 
## Solyc06g048450.2.1 Solyc02g011990.1.1 Solyc04g011960.1.1 
##                491                496                505 
## Solyc01g088020.2.1 Solyc07g009180.1.1 Solyc08g006230.2.1 
##                506                510                513 
## Solyc12g062480.1.1 Solyc09g074750.2.1 Solyc01g087310.2.1 
##                515                532                533 
## Solyc02g088140.1.1 Solyc01g096990.2.1 Solyc06g009970.2.1 
##                533                534                535 
## Solyc06g059930.2.1 Solyc07g018350.2.1 Solyc10g009590.2.1 
##                541                542                543 
## Solyc09g018370.2.1 Solyc09g091990.2.1 Solyc07g065790.2.1 
##                552                554                567 
## Solyc01g111950.2.1 Solyc07g066140.1.1 Solyc11g043130.1.1 
##                568                572                572 
## Solyc02g093380.1.1 Solyc07g042970.2.1 Solyc05g023840.1.1 
##                576                576                581 
## Solyc11g039870.1.1 Solyc10g006480.1.1 Solyc02g090140.1.1 
##                581                585                587 
## Solyc09g074690.2.1 Solyc03g116830.2.1 Solyc01g100310.2.1 
##                594                597                608 
## Solyc01g058160.2.1 Solyc08g075670.1.1 Solyc05g010100.2.1 
##                619                628                631 
## Solyc08g007600.1.1 Solyc06g082040.1.1 Solyc08g065710.1.1 
##                637                640                646 
## Solyc01g110820.2.1 Solyc06g062750.2.1 Solyc12g038590.1.1 
##                659                660                660 
## Solyc02g070750.1.1 Solyc01g110770.2.1 Solyc07g054630.2.1 
##                662                667                673 
## Solyc01g111140.2.1 Solyc01g091060.1.1 Solyc01g105590.2.1 
##                678                681                681 
## Solyc04g049580.2.1 Solyc11g008050.1.1 Solyc06g010090.1.1 
##                686                691                693 
## Solyc03g112950.2.1 Solyc03g110890.1.1 Solyc04g026280.2.1 
##                694                695                695 
## Solyc11g044250.1.1 Solyc12g096800.1.1 Solyc12g041960.1.1 
##                697                697                706 
## Solyc08g077140.1.1 Solyc08g066120.2.1 Solyc04g051570.2.1 
##                714                719                722 
## Solyc09g005330.2.1 Solyc12g021190.1.1 Solyc01g111220.2.1 
##                723                723                726 
## Solyc08g080810.1.1 Solyc03g116940.1.1 Solyc11g044960.1.1 
##                734                737                777 
## Solyc04g014430.1.1 Solyc01g106780.2.1 Solyc12g013600.1.1 
##                789                812                819 
## Solyc02g093200.2.1 Solyc07g053120.2.1 Solyc02g091770.1.1 
##                838                841                849 
## Solyc02g068780.2.1 Solyc01g091070.2.1 Solyc02g086340.2.1 
##                858                876                885 
## Solyc09g098250.2.1 Solyc05g050630.2.1 Solyc07g005800.2.1 
##                908                941                948 
## Solyc02g087170.2.1 Solyc04g028560.2.1 Solyc01g014520.1.1 
##                963                973                975 
## Solyc02g036270.2.1 Solyc06g049100.2.1 Solyc10g084320.1.1 
##                976                979                983 
## Solyc01g091120.2.1 Solyc01g058010.2.1 Solyc01g091080.2.1 
##                990                996               1042 
## Solyc05g014730.1.1 Solyc04g008310.1.1 Solyc03g093850.1.1 
##               1082               1085               1111 
## Solyc03g006550.2.1 Solyc01g111030.1.1 Solyc08g074740.2.1 
##               1116               1120               1123 
## Solyc01g097930.2.1 Solyc01g111060.2.1 Solyc07g018000.2.1 
##               1167               1176               1183 
## Solyc07g043640.2.1 Solyc01g106980.1.1 Solyc08g005860.2.1 
##               1190               1274               1307 
## Solyc03g097290.2.1 Solyc10g084140.1.1 Solyc01g094060.2.1 
##               1317               1325               1328 
## Solyc12g013680.1.1 Solyc01g005760.2.1 Solyc08g016050.2.1 
##               1382               1391               1392 
## Solyc01g105830.2.1 Solyc02g014190.2.1 Solyc02g079630.1.1 
##               1412               1540               1548 
## Solyc03g058550.1.1 Solyc01g110960.2.1 Solyc07g043620.2.1 
##               1563               1830               1950 
## Solyc04g049930.2.1 Solyc01g110010.2.1 Solyc01g111050.2.1 
##               2147               2393               2502 
## Solyc05g054880.2.1 Solyc04g076510.2.1 Solyc01g060040.2.1 
##               2883               2942               2972 
## Solyc04g050520.2.1 Solyc01g088170.2.1 
##               3713               9272

5 examples of genes with mismapping

  • Solyc02g090930.2.1 (12): Tandem Repeat with Solyc02g090940.2.1
  • Solyc04g072480.2.1 (30): Nothing obviously strange
  • Solyc03g051930.2.1 (70): PEN gene spans two LYC genes
  • Solyc02g079850.2.1 (150): PEN gene spans two LYC genes
  • Solyc01g110960.2.1 (497): Much Confusion

5 examples of genes with zero mapping

##                 lyc.id count.known gene.length.ratio.pen.lyc
## 56    Solyc00g014800.1         209                 0.8963415
## 81    Solyc00g039290.1           3                 0.5263158
## 82    Solyc00g042130.1         641                 0.7219858
## 110   Solyc00g097260.1           1                 0.7368421
## 112   Solyc00g099160.1         111                 1.0512821
## 146   Solyc00g269810.1          13                 1.1600000
## 149   Solyc00g304030.1         271                 0.8714154
## 267   Solyc01g006410.2         196                 0.7125749
## 334   Solyc01g007220.2         243                 1.0000000
## 549   Solyc01g010460.2         125                 0.2624672
## 585   Solyc01g011150.1         665                 0.9316770
## 603   Solyc01g014740.1           1                 0.9662921
## 623   Solyc01g017870.1          51                 1.0000000
## 635   Solyc01g021700.1         750                 0.7780679
## 646   Solyc01g028930.2         231                 0.9460784
## 672   Solyc01g056280.2         875                 0.9707447
## 711   Solyc01g057890.1         144                 0.8735632
## 753   Solyc01g060020.2         456                 1.0000000
## 803   Solyc01g066420.2          16                 1.0000000
## 1184  Solyc01g081580.1          59                 1.1300813
## 1311  Solyc01g088470.2          64                 0.6506849
## 2018  Solyc01g100100.2          47                 1.0441176
## 2403  Solyc01g106240.2         786                 1.0015987
## 2404  Solyc01g106250.2        1715                 0.9643917
## 2439  Solyc01g106660.1         352                 0.8213925
## 2752  Solyc01g110750.2         250                 1.2406015
## 2756  Solyc01g110860.1          71                 0.9901961
## 2806  Solyc01g111480.1         734                 0.2129514
## 2924  Solyc02g014520.2          59                 0.7622378
## 3007  Solyc02g030630.1          19                 1.2508143
## 3058  Solyc02g036230.1           3                 0.8791209
## 3234  Solyc02g064620.2         107                 0.3187773
## 3613  Solyc02g070650.2          45                 1.0000000
## 4139  Solyc02g081560.1           5                 1.0447761
## 4356  Solyc02g084360.2         109                 1.0000000
## 4841  Solyc02g090590.1           3                 0.8674699
## 5062  Solyc02g093250.2           1                 1.0000000
## 5236  Solyc03g005560.1         239                 0.9962193
## 5811  Solyc03g046170.1          42                 0.6637931
## 5897  Solyc03g062850.1         229                 1.0626058
## 5933  Solyc03g063820.1          62                 0.9889706
## 5939  Solyc03g063980.1         132                 0.8737374
## 5982  Solyc03g078340.1          44                 0.7068966
## 6283  Solyc03g096140.1         305                 1.0000000
## 6284  Solyc03g096170.1         145                 1.2187500
## 6294  Solyc03g096530.1          22                 0.8476821
## 6476  Solyc03g110850.1           1                 1.1341463
## 7055  Solyc03g117880.1         769                 1.0705882
## 7685  Solyc04g008310.1        1102                 0.9830149
## 8062  Solyc04g018210.1          54                 0.7954545
## 8065  Solyc04g024420.2         195                 0.9890511
## 8070  Solyc04g024690.1          25                 0.6496350
## 8074  Solyc04g024880.1          59                 0.3733333
## 8113  Solyc04g028500.1          66                 0.5776173
## 8127  Solyc04g040140.1          87                 0.5433071
## 8135  Solyc04g045320.1         128                 1.2435897
## 8181  Solyc04g049520.1         315                 1.0841121
## 8197  Solyc04g049900.1         856                 1.0727969
## 8241  Solyc04g051000.1          57                 0.8461538
## 8287  Solyc04g052970.1          66                 0.8846154
## 8347  Solyc04g055070.1           8                 1.0928571
## 8677  Solyc04g074910.2          23                 1.0000000
## 9358  Solyc05g006290.1         233                 0.4068100
## 9437  Solyc05g007250.2         492                 1.0000000
## 9663  Solyc05g010220.1         250                 0.9232737
## 9674  Solyc05g010360.1          70                 1.0118483
## 9873  Solyc05g014100.1         362                 0.3647343
## 10044 Solyc05g023850.1         104                 0.6029412
## 10068 Solyc05g025720.1         624                 1.0692308
## 10150 Solyc05g046180.1          69                 1.0000000
## 10228 Solyc05g050640.1          53                 0.9408602
## 10381 Solyc05g052810.2         318                 0.5255814
## 10439 Solyc05g053460.1          99                 1.0370370
## 10864 Solyc06g008550.1          58                 0.7043478
## 10961 Solyc06g011500.1          71                 0.8878505
## 10975 Solyc06g017930.1          15                 0.6832298
## 11076 Solyc06g043010.1          32                 0.6553191
## 11129 Solyc06g049100.2         980                 1.0347826
## 11411 Solyc06g060470.1           2                 1.0414938
## 11524 Solyc06g062900.2          40                 0.3236515
## 11590 Solyc06g064630.2         370                 1.0000000
## 11685 Solyc06g065980.2          96                 1.0000000
## 12471 Solyc06g082600.2          68                 1.0000000
## 12866 Solyc07g007770.1         138                 0.4929577
## 12979 Solyc07g009510.1         370                 1.0000000
## 12989 Solyc07g014690.2          17                 0.8848921
## 13002 Solyc07g016110.1           6                 0.8452381
## 13034 Solyc07g017930.1         190                 0.6250000
## 13072 Solyc07g021050.1          21                 0.5917160
## 13079 Solyc07g021490.1         172                 0.4699454
## 13159 Solyc07g039630.1          13                 1.1021898
## 14050 Solyc07g064780.1          24                 0.4800000
## 14314 Solyc08g006260.1         471                 0.7976190
## 14564 Solyc08g015710.1         760                 1.1536797
## 14584 Solyc08g016290.1         182                 1.0188172
## 14619 Solyc08g023560.2           1                 0.4531590
## 14640 Solyc08g036480.1         692                 1.0582960
## 14743 Solyc08g061810.2         358                 0.9494382
## 14792 Solyc08g062980.1         120                 1.1464968
## 14941 Solyc08g067520.1          52                 0.9674797
## 14949 Solyc08g067650.1         303                 0.7388535
## 15031 Solyc08g069080.2          23                 1.0000000
## 15057 Solyc08g074460.1         211                 1.0868321
## 15669 Solyc08g082380.1          57                 1.1188811
## 15730 Solyc08g083120.2         193                 1.0000000
## 16011 Solyc09g009310.1          36                 0.7797927
## 16257 Solyc09g014700.1           8                 0.4285714
## 16341 Solyc09g020080.1         166                 0.9132231
## 16358 Solyc09g030430.1         372                 1.2943548
## 16411 Solyc09g055690.1          23                 0.7156863
## 16440 Solyc09g057700.1         647                 1.1433692
## 16493 Solyc09g061350.1          15                 1.0636364
## 16501 Solyc09g061530.1         115                 1.1142857
## 16554 Solyc09g064660.2         213                 1.0000000
## 16650 Solyc09g066030.1         310                 0.3950276
## 16942 Solyc09g082840.1         484                 1.1594203
## 17084 Solyc09g090610.2         290                 1.0000000
## 17144 Solyc09g091350.1         212                 0.9142857
## 17444 Solyc10g006480.1         681                 1.0000000
## 17587 Solyc10g008260.1         277                 1.0308370
## 17636 Solyc10g008910.1           2                 1.0000000
## 17724 Solyc10g012390.1         433                 1.1666667
## 17790 Solyc10g026520.1         957                 1.0612245
## 17819 Solyc10g044550.1         190                 0.8170732
## 17839 Solyc10g045230.1           3                 0.8400000
## 17859 Solyc10g046790.1          68                 1.0875000
## 17956 Solyc10g050530.1        1092                 1.0983146
## 18069 Solyc10g061970.1          27                 1.0000000
## 18124 Solyc10g076170.1          21                 0.4916201
## 18532 Solyc10g083280.1         184                 1.0000000
## 18624 Solyc10g084480.1          94                 1.0619469
## 19151 Solyc11g010230.1          70                 1.0000000
## 19309 Solyc11g012380.1          60                 0.8581081
## 19397 Solyc11g013550.1           1                 1.0000000
## 19462 Solyc11g019860.1         297                 0.9572368
## 19497 Solyc11g021130.1          16                 0.4615385
## 19528 Solyc11g030670.1           8                 0.9112426
## 19577 Solyc11g042470.1         209                 0.3085847
## 19614 Solyc11g044610.1          45                 0.5860215
## 19646 Solyc11g045370.1           4                 1.0200000
## 19649 Solyc11g045510.1          18                 0.5431472
## 19659 Solyc11g050860.1         303                 1.1878788
## 19670 Solyc11g056540.1         131                 1.2633333
## 19709 Solyc11g063590.1         588                 1.0473934
## 20004 Solyc11g069730.1           6                 0.9266055
## 20179 Solyc11g072860.1         114                 1.0000000
## 20412 Solyc12g008480.1          26                 0.3364780
## 20482 Solyc12g009330.1         167                 1.0000000
## 20516 Solyc12g009870.1         247                 1.0666667
## 20552 Solyc12g010350.1           3                 0.7790698
## 20582 Solyc12g010760.1          49                 1.0000000
## 20815 Solyc12g019600.1          63                 0.7722772
## 20843 Solyc12g027710.1          55                 0.3580247
## 20863 Solyc12g035300.1          27                 0.4264151
## 20936 Solyc12g040270.1          18                 0.7435897
## 20947 Solyc12g040550.1         150                 1.1745455
## 21232 Solyc12g070170.1        1248                 1.1776062
## 21236 Solyc12g077350.1          62                 0.5458167
## 21635 Solyc12g099990.1           2                 1.2066667
  • Solyc01g010050.2: Two overlapping LYC transcripts (note this is fixed when using FeatureCounts from subread)
  • Solyc01g060020.2: Multiple overlapping LYC transcripts
  • Solyc05g023780.1: Repetitive region
  • Solyc08g015710.1: Very small region of homology
  • Solyc11g056540.1: BLAT did not find a match

How to deal with this?

Many of these issues could be dealt with by

  1. Eliminating genes with overlapping LYC to LYC or PEN to LYC transcripts.
  2. Using the BLAT results to eliminate transcripts with poor homology.

Original

## [1] 0.9376397

With bad annotations removed

Genes where more than one S.lyc or more than one S.pen annotation overlap are removed.

with(pen.count.comparison.1[pen.count.comparison.1$flag=="none",],cor(count.known,count.mapped))
## [1] 0.9814712

Pretty good!

Mapping to cDNA reference with kallisto

installation

mac command line

brew install kallisto

build index

only needs to be done once:

kallisto index -i ITAG2.4._cds.pen.orthlogsonly.31.kai ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta

But I wonder if different kmers would give different results

For kallisto fasta needs to be converted to fastq

Download converter

gzcat  spen_sim_2/sample_01_renamed.fasta.gz | perl ~/bin/fasta_to_fastq.pl  - | gzip > spen_sim_2/sample_01_renamed.fastq.gz
gzcat  slyc_sim_2/sample_01_renamed.fasta.gz | perl ~/bin/fasta_to_fastq.pl  - | gzip > slyc_sim_2/sample_01_renamed.fastq.gz

run kallisto

RunKallisto(fasta = "spen_sim_2/sample_01_renamed.fastq.gz", index = "ITAG2.4._cds.pen.orthlogsonly.31.kai", dir = "spen_sim_2/kallisto31" )

Load in mapped counts

pen.mapped.counts <- GetMappedCounts(dir = "spen_sim_2/kallisto", type="kallisto-transcripts")

S. pennellii

Compare known to mapped counts

Remove overlapping genes and plot

Genes with more than one S.lyc or more than one S.pen annotation overlap are removed.

Pretty good!

Kallisto with 21nt kmers

build index

only needs to be done once:

kallisto index -k 21 -i ITAG2.4._cds.pen.orthlogsonly.21.kai ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta

run kallisto

RunKallisto(fasta = "spen_sim_2/sample_01_renamed.fastq.gz", index = "ITAG2.4._cds.pen.orthlogsonly.21.kai", dir = "spen_sim_2/kallisto21" )

Load in mapped counts

pen.mapped.counts <- GetMappedCounts(dir = "spen_sim_2/kallisto21", type="kallisto-transcripts")

S. pennellii

Compare known to mapped counts

Remove overlapping genes and plot

Genes with more than one S.lyc or more than one S.pen annotation overlap are removed.

Pretty good!

Optimize Kallisto kmer

Idea

Lowering the kallisto kmer improved the correlation between known and mapped counts

What is the best kmer?

In this section I will try a bunch of kmers

Build kalliso indexes for different kmers.

#only run once...it will be slow!
library(snowfall)
kmers <- c(seq(11,19,2),seq(23,29,2)) #21 and 31 already done
sfInit(cpu=min(kmers,12),parallel = TRUE)
sfClusterApply(kmers, function(k) {
  index.name <- paste("ITAG2.4._cds.pen.orthlogsonly.",k,".kai",sep="")
  system(paste("kallisto index -k", k,
               " -i", index.name, 
               "~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_cds.pen.orthologs.only.fasta"))})
sfStop()

Run Kallisto on the different indicies

library(snowfall)
## Loading required package: snow
## 
## Attaching package: 'snow'
## The following objects are masked from 'package:BiocGenerics':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, clusterSplit, parApply, parCapply,
##     parLapply, parRapply, parSapply
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, clusterSplit, makeCluster,
##     parApply, parCapply, parLapply, parRapply, parSapply,
##     splitIndices, stopCluster
indicies <- dir(pattern="[0-9]\\.kai")
sfInit(cpu=2,parallel = TRUE)
## Warning in searchCommandline(parallel, cpus = cpus, type = type,
## socketHosts = socketHosts, : Unknown option on commandline:
## rmarkdown::render('/Users/jmaloof/Documents/Lab~+~Notebook~+~support/2015/
## rnaseq_simulations/Spen_rnaseq_simulation_full.Rmd',~+~~+~encoding~+~
## R Version:  R version 3.2.3 (2015-12-10)
## snowfall 1.84-6.1 initialized (using snow 0.4-1): parallel execution on 2 CPUs.
sfSource("Rnaseq_sim_helper_functions.R")
## Source Rnaseq_sim_helper_functions.R loaded.
## Source Rnaseq_sim_helper_functions.R loaded in cluster.
## 
## > RunStar <- function(fasta, prefix, param.file = "../STAR.params.whitney.1", 
## +     args = "", dir = ".", twopassMode = "Basic", n = 12) {
## +     old. .... [TRUNCATED] 
## 
## > RunKallisto <- function(fasta, index, dir) {
## +     bampath <- file.path(dir, "kallisto.bam")
## +     system(paste("kallisto quant --single --plaintext ..." ... [TRUNCATED] 
## 
## > GetMappedCounts <- function(prefix = NA, dir = ".", 
## +     type = "STAR", gff = "~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/ITAG2.4_gene_model ..." ... [TRUNCATED] 
## 
## > CompareCounts <- function(known.counts, mapped.counts = NA, 
## +     title = NULL, plot = TRUE, chrom.separate = TRUE, correlation = TRUE, 
## +     retu .... [TRUNCATED] 
## 
## > PSL2Granges <- function(file) {
## +     psl.data <- read.delim(file, header = FALSE, skip = 5)
## +     psl.header <- make.names(apply(read.delim(file, h .... [TRUNCATED]
sfExport("pen.known.counts","lyc.lyc.overlaps","pen.pen.overlaps","pen.gene.length","lyc.gene.length")
results.combined <- sfLapply(indicies,function(i) {
  kmer <- sub("ITAG2\\.4\\._cds\\.pen\\.orthlogsonly\\.([0-9]{2})\\.kai","\\1",i)
  dir.out <- paste("spen_sim_2/kallisto",kmer,sep="")
  results <- list()
  results$kmer <- as.numeric(kmer)
  results$time <- system.time(RunKallisto(fasta = "spen_sim_2/sample_01_renamed.fastq.gz", 
              index = i, 
              dir = dir.out))
  pen.mapped.counts <- GetMappedCounts(dir = dir.out, type="kallisto-transcripts")
  pen.count.comparison <- CompareCounts(pen.known.counts,pen.mapped.counts,plot = FALSE,correlation = FALSE)
  pen.count.comparison$flag <- "none"
  pen.count.comparison <- within(pen.count.comparison,{
                                 flag[pen.count.comparison$lyc.id %in% lyc.lyc.overlaps] <- "lyc.lyc.overlap"
                                 flag[pen.count.comparison$lyc.id %in% pen.pen.overlaps] <- "pen.pen.overlap"
                                 }
                                 )
  results$corr.all <- with(pen.count.comparison,c(cor(count.known, count.mapped),cor(count.known,count.mapped,method="spearman")))
  results$corr.bad.removed <- with(pen.count.comparison[pen.count.comparison$flag=="none",],
                                   c(cor(count.known, count.mapped),cor(count.known,count.mapped,method="spearman")))
  return(results)
})
sfStop()
## 
## Stopping cluster

kalliso kmer effects

So, kmer=19 is the best

Mapping to genomic with subread

Installation

Download subread

untar and unzip it, move binaries to /usr/local/bin (or make symbolic links)

# in R
install.pacakges("Rsubread")

Build Indexes

library(Rsubread)
buildindex("Slyc_Chromo2.5_subread_index","/Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/S_lycopersicum_chromosomes.2.50.fa") #note does not do tilde expansion
# 5.5 minutes

Map

system.time(align("Slyc_Chromo2.5_subread_index",
                  "spen_sim_2/sample_01_renamed.fastq.gz", 
                  output_file=paste("spen_sim_2/sample_01_renamed.fastq.gz","subread","default","BAM",sep="."),
                  nthreads = 2))

On Royce, with 2 threads:

user system elapsed
310.463 32.216 211.111

Get Counts

pen.mapped.counts <- GetMappedCounts(dir="spen_sim_2/",type = "featureCounts",bam = "sample_01_renamed.fastq.gz.subread.default.BAM")
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.20.2
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           S spen_sim_2//sample_01_renamed.fastq.gz.sub ... ||
## ||                                                                            ||
## ||             Output file : ./.Rsubread_featureCounts_pid88215               ||
## ||             Annotations : /Users/jmaloof/Sequences/ref_genomes/tomato/ ... ||
## ||                                                                            ||
## ||                 Threads : 2                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : counted                                          ||
## ||       Read orientations : fr                                               ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2 ... ||
## ||    Features : 160001                                                       ||
## ||    Meta-features : 34725                                                   ||
## ||    Chromosomes/contigs : 13                                                ||
## ||                                                                            ||
## || Process BAM file spen_sim_2//sample_01_renamed.fastq.gz.subread.defaul ... ||
## ||    Single-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 9901756                                                   ||
## ||    Successfully assigned reads : 8803449 (88.9%)                           ||
## ||    Running time : 0.20 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//

Compare counts

Compare known to mapped counts

Remove overlapping genes and compare

Genes with more than one S.lyc or more than one S.pen annotation overlap are removed.

map with subread allowing more mismatches (5)

system.time(align("Slyc_Chromo2.5_subread_index",
                  "spen_sim_2/sample_01_renamed.fastq.gz", 
                  output_file=paste("spen_sim_2/sample_01_renamed.fastq.gz","subread","5MM","BAM",sep="."),
                  nthreads = 2,
                  maxMismatches = 5))

On Royce, with 2 threads:

user system elapsed
315.772 29.543 221.174
pen.mapped.counts <- GetMappedCounts(dir="spen_sim_2/",type = "featureCounts",bam = "sample_01_renamed.fastq.gz.subread.5MM.BAM")
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.20.2
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           S spen_sim_2//sample_01_renamed.fastq.gz.sub ... ||
## ||                                                                            ||
## ||             Output file : ./.Rsubread_featureCounts_pid88215               ||
## ||             Annotations : /Users/jmaloof/Sequences/ref_genomes/tomato/ ... ||
## ||                                                                            ||
## ||                 Threads : 2                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : counted                                          ||
## ||       Read orientations : fr                                               ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2 ... ||
## ||    Features : 160001                                                       ||
## ||    Meta-features : 34725                                                   ||
## ||    Chromosomes/contigs : 13                                                ||
## ||                                                                            ||
## || Process BAM file spen_sim_2//sample_01_renamed.fastq.gz.subread.5MM.BA ... ||
## ||    Single-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 9901756                                                   ||
## ||    Successfully assigned reads : 8804555 (88.9%)                           ||
## ||    Running time : 0.19 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//

Compare counts

Compare known to mapped counts

Remove overlapping genes and compare

Genes with more than one S.lyc or more than one S.pen annotation overlap are removed.

Map with bowtie2

Installation

brew install bowtie2

Make bowtie index

bowtie2-build --threads 2 ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/S_lycopersicum_chromosomes.2.50.fa ~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/S_lycopersicum_chromosomes.2.50.fa

Map

system.time(RunBowtie2(fastq = "spen_sim_2/sample_01_renamed.fastq.gz",
           index = "~/Sequences/ref_genomes/tomato/ITAG2.4_Chromo2.5/S_lycopersicum_chromosomes.2.50.fa",
           dir = "spen_sim_2/"))

Royce with 2 threads user | system | elapsed ——–|——–|——–
622.348 | 13.297 | 300.922

Get counts

pen.mapped.counts <- GetMappedCounts(dir="spen_sim_2/",type = "featureCounts",bam = "bowtie2.bam")
## 
##         ==========     _____ _    _ ____  _____  ______          _____  
##         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
##           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
##             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
##               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
##         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
##        Rsubread 1.20.2
## 
## //========================== featureCounts setting ===========================\\
## ||                                                                            ||
## ||             Input files : 1 BAM file                                       ||
## ||                           S spen_sim_2//bowtie2.bam                        ||
## ||                                                                            ||
## ||             Output file : ./.Rsubread_featureCounts_pid89516               ||
## ||             Annotations : /Users/jmaloof/Sequences/ref_genomes/tomato/ ... ||
## ||                                                                            ||
## ||                 Threads : 2                                                ||
## ||                   Level : meta-feature level                               ||
## ||              Paired-end : no                                               ||
## ||         Strand specific : no                                               ||
## ||      Multimapping reads : not counted                                      ||
## || Multi-overlapping reads : counted                                          ||
## ||       Read orientations : fr                                               ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//
## 
## //================================= Running ==================================\\
## ||                                                                            ||
## || Load annotation file /Users/jmaloof/Sequences/ref_genomes/tomato/ITAG2 ... ||
## ||    Features : 160001                                                       ||
## ||    Meta-features : 34725                                                   ||
## ||    Chromosomes/contigs : 13                                                ||
## ||                                                                            ||
## || Process BAM file spen_sim_2//bowtie2.bam...                                ||
## ||    Single-end reads are included.                                          ||
## ||    Assign reads to features...                                             ||
## ||    Total reads : 9901756                                                   ||
## ||    Successfully assigned reads : 9107218 (92.0%)                           ||
## ||    Running time : 0.29 minutes                                             ||
## ||                                                                            ||
## ||                         Read assignment finished.                          ||
## ||                                                                            ||
## \\===================== http://subread.sourceforge.net/ ======================//

Compare counts

Compare known to mapped counts

Remove overlapping genes and compare

Genes with more than one S.lyc or more than one S.pen annotation overlap are removed.